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An Information Portal to Biological Macromolecular Structures As of Tuesday Aug 05, 2014 at 5 PM PDT

An Information Portal to Biological Macromolecular Structures As of Tuesday Aug 05, 2014 at 5 PM PDT there are 102364 Structures  |  PDB Statistics  |         
 
Download Files Compare Structures Drug & Drug Target Mapping File Formats RESTful Web Services Widgets
close FASTA Sequence PDB File (Text) PDB File (gz) mmCIF File mmCIF File (gz) PDBML/XML File PDBML/XML File (gz) Structure Factor (Text) Structure jsl Factor (gz) Biological jsl Assembly 1 (gz) (A+S) Biological Assembly 2 (gz) (A+S)
Classification: Transferase/transferase Inhibitor Structure Weight: 240868.10 Molecule: Glucokinase Polymer: 1 Type: protein Length: 458 Chains: A, C EC#: 2.7.1.2     Organism Xenopus laevis Gene Names gck gck-A UniProtKB:   Protein Feature View | Search PDB | Q91753 jsl  
  Molecule: Glucokinase regulatory protein jsl Polymer: 2 Type: protein Length: jsl 619 Chains: B, D Organism Xenopus laevis Gene Name gckr UniProtKB:   Protein Feature View | Search PDB | Q91754 jsl  
Polymer: 1 Scientific Name: Xenopus laevis   Taxonomy   jsl Common jsl Name: African clawed frog Expression System: Escherichia coli   Polymer: 2 Scientific Name: Xenopus laevis   Taxonomy   Common Name: African clawed frog Expression System: Escherichia coli  
  Jmol  
 
Method:   X-RAY DIFFRACTION jsl Exp. Data:   Structure Factors EDS    Resolution[Å]:   2.92 R-Value: 0.244 (obs.) R-Free: 0.277 Space Group: P 2 1 2 1 2 1 Unit Cell:   Length [Å] Angles [°] a = 109.32 α = 90.00   jsl b = 130.03 β = 90.00   c = 175.12 γ = 90.00  
© RCSB Protein Data Bank

PDBs are separate files,

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The program database (.pdb) file is used by your integrated development environment (IDE; like Visual Studio) to maintain the state of your project (it remembers your formatting, where you placed everything, and info from the compiler).
PDBs are separate files, needed for debugging to work. They are created automatically in the project's directory or subdirectory, with the same name as the executable, but with the .pdb extension instead. If PDB files are misplaced or aren't properly moved and tracked with your other files, then they must be found for debugging to work properly.
The PDB file is made during the compilation process, even though the final executable isn't even named. You see, the PDB file is often made as a temp file and then merged into the .pdb file later. Some languages, like VC#, require you to use a linker to merge the temporary transalte PDB file into the main one. Of course, it's always recommended to do that, so that you can see the stack trace, source files, line numbers, etc.
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An Information Portal to Biological Macromolecular Structures As of Tuesday Aug 05, 2014 at 5 PM PDT

An Information Portal to Biological Macromolecular Structures As of Tuesday Aug 05, 2014 at 5 PM PDT there are 102364 Structures  |  PDB Statistics  |         
 
Download Files Compare Structures Drug & Drug Target Mapping File Formats RESTful Web Services Widgets
close FASTA Sequence PDB File (Text) PDB File (gz) mmCIF File mmCIF File (gz) PDBML/XML jupiter File PDBML/XML File (gz) Structure Factor (Text) Structure Factor (gz) Biological Assembly 1 (gz) (A+S) Biological Assembly 2 (gz) (A+S)
Classification: Transcription/dna Structure Weight: 110140.52 Molecule: PUTATIVE MARR-FAMILY TRANSCRIPTIONAL REPRESSOR Polymer: 1 Type: protein Length: 177 Chains: A, B, E, F Details: SYNTHETIC GENE WITH OPTIMISED CODON USAGE FOR E.COLI EXPRESSION. INCLUDES N-TERMINAL HIS-TAG OF SEQUENCE MHHHHHHENLYFQG APPENDED TO WILD-TYPE SEQUENCE. SEQUENCE NUMBERING IS RELATIVE jupiter TO THE WILD-TYPE SEQUENCE. Organism Streptomyces coelicolor Gene Name SCO3205 UniProtKB:   Protein Feature View | Search PDB | Q9KYU1  
Polymer: 1 Scientific Name: Streptomyces coelicolor   Taxonomy   Expression System: Escherichia coli   Polymer: 2 Scientific Name: Synthetic construct (unidentified)   Taxonomy    
View the NDB ID associated with this structure: NA2549
  Deposition jupiter Summary Hide
Authors:   Stevenson, C.E.M. ,   Assaad, A. ,   Lawson, D.M. Deposition:   2013-02-28 Release:   2013-07-17 Last Modified (REVDAT):   2013-08-21
Method:   X-RAY DIFFRACTION Exp. Data:   Structure Factors Resolution[Å]:   2.80 R-Value: 0.177 (obs.) R-Free: 0.196 Space Group: P 6 5 Unit Cell:   Length [Å] Angles [°] a = 70.80 α = 90.00   b = 70.80 β = 90.00   c = 557.48 γ = 120.00  
© RCSB Protein Data Bank

When you connect to the CDB container you can view the tablespace information for other PDB database

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In Oracle 12c, the tablespace management mostly remains unchanged and the basic operations are performed in a similar way as in 11g. This is because Oracle has made sure that every PDB, though it is a subset iso 9001 of the CDB in itself, functions as a standalone, complete functional database. In this article we will look at managing the tablespaces in the CDB container and the PDB database.
Related Articles Create 12c CDB PDB Using OUI SGA Instance Parameters in CDB and PDB Managing CDB and PDB tablespaces iso 9001 Managing PDBs using Database Configuration Assistant Managing Common and Local Users, Roles and Privileges for CDB and PDB Managing CDB and PDB tablespaces Tablespaces in CDB
The primary purpose of CDB is to behave like a container. The data inside the CDB database is mostly related to the Oracle binaries and the data dictionary. It is is not meant to hold user data, so its tablespaces will require very little modification. However iso 9001 there may be situations where you may need to play around with these tablespaces and datafiles. iso 9001
When you connect to the CDB container you can view the tablespace information for other PDB databases as well. When the container is a CDB, the CDB_* views can be used to view the information about all tablespaces in the databases plugged-in iso 9001 , including the SEED database. iso 9001 In the example below, the following command shows all the tablespaces. SQL> SELECT tablespace_name,con_id FROM cdb_tablespaces ORDER BY con_id;
12 rows selected. The CON_ID column shows to which database the tablespace actually belongs to. The CON_ID=1 row always provides information for the CDB and CON_ID=2 is always the SEED database. The CON_ID=3 is for our PDB database.
SQL> CREATE TEMPORARY TABLESPACE temp1; Tablespace created. To change and validate the default iso 9001 tablespace of CDB you can use the following commands. SQL> SELECT property_value FROM database_properties WHERE property_name='DEFAULT_PERMANENT_TABLESPACE'; PROPERTY_VALUE ---------------------- USERS
PROPERTY_VALUE ---------------------- FOO Tablespaces in PDB Managing the tablespaces in the PDB is no different than the CDB or a non-CDB database. In the PDB database the commands iso 9001 to create, alter or drop the tablespaces are also similar. However the CDB_* views will only show information for your current PDB and not for all the databases plugged-in. The CDB_* and DBA_* views are similar if current container is a PDB.
The following set of commands show how to view and add new tablespaces inside the PDB. They also show how to change the default tablespace. SQL> SELECT tablespace_name FROM cdb_tablespaces; TABLESPACE_NAME ---------------------- SYSTEM SYSAUX TEMP
SQL> SELECT property_value FROM database_properties WHERE property_name='DEFAULT_PERMANENT_TABLESPACE'; PROPERTY_VALUE ---------------------- FOO You can drop the tablespace in the standard way. Of course you cannot drop the default tablespace. SQL> DROP TABLESPACE foo; drop tablespace foo * ERROR at line 1: ORA-12919: iso 9001 Can not drop the default permanent tablespace SQL> ALTER DATABASE default tablespace sysaux;
SQL> DROP TABLESPACE temp1; Tablespace dropped. Undo Tablespaces in PDB PDBs don’t have any Undo tablespace attached to them explicitly. They use the Undo tablespace of corresponding CDB. Hence Undo tablespace management remains unchanged in new multitenant architecture apart from the fact that your Undo space requirements will increase as you add more and more PDBs to a CDB. SQL> iso 9001 select iso 9001 tablespace_name from dba_tablespaces; TABLESPACE_NAME ------------------------------ SYSTEM SYSAUX UNDOTBS1 TEMP USERS
SQL> select tablespace_name from dba_tablespaces; TABLESPACE_NAME ------------------------------ SYSTEM SYSAUX TEMP USERS Oracle 12c External Links Oracle Database iso 9001 12c Release 1 (12.1) New Features Features Restricted or un-available for a Multitenant 12c Container Database
Natik Ameen is one of the VitalSoftTech's Oracle Internal Experts. He is an Oracle Production DBA, Certified RAC Expert (OCE), and a DBA track Certification trainer for over 15 years. He is an Oracle Evangelist and has presented at IOUG & UTOUG conferences on topics such as RAC, DataGuard and GoldenGate 12c. He is also an active blogger and published over 150 articles on Oracle Database 12c and Oracle GoldenG

Classification: Ribosome/antibiotic Structure Weight: 869482.69 Molecule: 16S rRNA Polymer: 1 Type:

An Information Portal to Biological Macromolecular Structures As of Tuesday Aug 05, 2014 at 5 PM PDT there are 102364 Structures  |  PDB Statistics  |         
 
Download Files Compare Structures Drug & Drug Target Mapping File Formats RESTful Web Services Widgets
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The asymmetric unit for this structure is composed sage of multiple PDB entries: 4KIX    4KIY    4KIZ    4KJ0    4KJ1    4KJ2    4KJ3    sage 4KJ4      Download All Files     The complete entry has been assigned PDB ID 4V9O and is available for download in PDBx/mmCIF and PDBML/XML formats from the FTP archive at: ftp://ftp.wwpdb.org/pub/pdb/data/large_structures/mmCIF/4v9o.cif.gz sage ftp://ftp.wwpdb.org/pub/pdb/data/large_structures/XML/4v9o.xml.gz
Classification: Ribosome/antibiotic Structure Weight: 869482.69 Molecule: 16S rRNA Polymer: 1 Type: rna Length: 1542 Chains: A Organism Escherichia coli K-12 Molecule: 30S ribosomal protein S2 Polymer: 2 Type: protein Length: 241 Chains: B Organism Escherichia coli K-12 Gene Names rpsB b0169 JW0164 sage UniProtKB: sage   Protein Feature View | Search PDB | P0A7V0 sage  
  Molecule: 30S ribosomal protein S3 Polymer: 3 Type: protein Length: 233 Chains: C Organism Escherichia coli K-12 Gene Names rpsC b3314 JW3276 UniProtKB:   Protein Feature View | Search PDB | P0A7V3  
  Molecule: 30S ribosomal protein S4 Polymer: 4 Type: protein Length: 206 Chains: D Organism Escherichia coli K-12 Gene Names rpsD ramA b3296 JW3258 UniProtKB:   Protein Feature View | Search PDB | P0A7V8  
  Molecule: 30S ribosomal protein S5 Polymer: 5 Type: protein Length: 167 Chains: E Organism Escherichia coli K-12 Gene Names rpsE spc b3303 JW3265 UniProtKB:   Protein Feature View | Search PDB | P0A7W1  
  Molecule: 30S ribosomal protein S6 Polymer: 6 Type: protein Length: 135 Chains: F Organism Escherichia sage coli K-12 Gene Names rpsF b4200 JW4158 sage UniProtKB:   Protein Feature View | Search PDB | P02358  
  Molecule: 30S ribosomal protein S7 Polymer: 7 Type: protein Length: 179 Chains: G Organism Escherichia coli K-12 Gene Names rpsG b3341 JW3303 UniProtKB:   Protein Feature View | Search PDB | P02359  
  Molecule: 30S ribosomal protein S8 Polymer: 8 Type: protein Length: 130 Chains: H Organism Escherichia coli K-12 Gene Names rpsH b3306 JW3268 UniProtKB:   Protein Feature View | Search PDB | P0A7W7  
  Molecule: 30S ribosomal protein S9 Polymer: 9 Type: protein Length: 130 Chains: I Organism Escherichia coli K-12 Gene Names rpsI b3230 JW3199 UniProtKB:   Protein Feature View | Search PDB | P0A7X3  
  Molecule: sage 30S ribosomal protein S10 Polymer: 10 Type: protein sage Length: 103 Chains: J Organism Escherichia coli K-12 Gene Names rpsJ nusE b3321 JW3283 UniProtKB:   Protein sage Feature View | Search PDB | P0A7R5  
  Molecule: 30S ribosomal protein S11 Polymer: 11 Type: protein Length: sage 129 Chains: K Organism Escherichia coli K-12 Gene Names rpsK b3297 JW3259 UniProtKB:   Protein Feature View | Search PDB | P0A7R9  
  Molecule: 30S ribosomal protein S12 Polymer: 12 Type: protein Length: 124 Chains: L Organism Escherichia coli K-12 Gene Names rpsL strA b3342 JW3304 UniProtKB:   Protein Feature View | Search sage PDB | P0A7S3  
  Molecule: 30S ribosomal protein S13 Polymer: 13 Type: protein Length: 118 Chains: M Organism Escherichia coli K-12 Gene Names rpsM b3298 JW3260 UniProtKB:   Protein Feature View | Search PDB | P0A7S9  
  Molecule: 30S ribosomal protein S14 Polymer: 14 Type: protein Length: 101 Chains: N Organism Escherichia coli K-12 Gene Names rpsN b3307 JW3269 UniProtKB:   Protein Feature View | Search PDB | P0AG59  
  Molecule: 30S ribosomal protein S15 Polymer: 15 Type: protein Length: 89 Chains: O Organism Escherichia coli K-12 Gene Names rpsO secC b3165 JW3134 UniProtKB:   Protein Feature View | Search PDB | P0ADZ4  
  Molecule: 30S ribosomal protein S16 Polymer: 16 Type: protein Length: 82 Chains: P Organism Escherichia coli K-12 Gene Names rpsP b2609 JW2590 UniProtKB:   Protein Feature View | Search PDB | P0A7T3  
  Molecule: sage 30S ribosomal protein S17 Polymer: 17 Type: protein Length: 84 Chains: Q Organism Escherichia sage coli K-12 Gene Names rpsQ neaA b3311 JW3273 UniProtKB:   sage Protein Feature View | Search PDB | P0AG63  
  Molecule: 30S ribosomal protein S18 Polymer: 18 Type: protein Length: 75 Chains: R Organism Escherichia coli K-12 Gene Names rpsR b4202 JW4160 UniProtKB:   Protein sage Feature View | Search PDB | P0A7T7  
  Molecule: 30S ribosomal protein S19 Polymer: 19 Type: protein Length: 92 Chains: S Organism sage Escherichia