2PPG | pdb_00002ppg

Crystal structure of putative isomerase from Sinorhizobium meliloti

• PDB DOI: https://doi.org/10.2210/pdb2PPG/pdb

• Classification: ISOMERASE
• Organism(s): Sinorhizobium meliloti 1021
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-04-30 Released: 2007-05-22 
• Deposition Author(s): Ramagopal, U.A., Toro, R., Dickey, M., Logan, C., Groshong, C., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 
  0.252 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.183 (Depositor) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of putative isomerase from Sinorhizobium meliloti.

Ramagopal, U.A., Toro, R., Dickey, M., Logan, C., Groshong, C., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 176.77 kDa 
• Atom Count: 11,799 
• Modeled Residue Count: 1,522 
• Deposited Residue Count: 1,596 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative isomerase	A, B, C, D	399	Sinorhizobium meliloti 1021	Mutation(s): 9  Gene Names: RA0374, SMa0708
UniProt
Find proteins for Q92ZS5 (Rhizobium meliloti (strain 1021)) Explore Q92ZS5  Go to UniProtKB:  Q92ZS5

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free:  0.252 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.183 (Depositor) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.154	α = 90
b = 150.829	β = 90
c = 147.649	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-22 
Deposition Author(s): Ramagopal, U.A., Toro, R., Dickey, M., Logan, C., Groshong, C., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2007-05-22
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.5: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.6: 2023-08-30
  Changes: Data collection, Database references, Refinement description
• Version 1.7: 2023-11-15
  Changes: Data collection
• Version 1.8: 2024-10-30
  Changes: Structure summary