3JYG | pdb_00003jyg

Crystal structure of uncharacterized protein WS1659 from Wolinella succinogenes

• PDB DOI: https://doi.org/10.2210/pdb3JYG/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Wolinella succinogenes
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-09-21 Released: 2009-10-13 
• Deposition Author(s): Ramagopal, U.A., Toro, R., 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: 1.95 Å
• R-Value Free: 
  0.233 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

Crystal structure of uncharacterized protein WS1659 from Wolinella succinogenes

Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 133.99 kDa 
• Atom Count: 9,710 
• Modeled Residue Count: 1,080 
• Deposited Residue Count: 1,128 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C, D, E, F	188	Wolinella succinogenes	Mutation(s): 0  Gene Names: WS1659 EC: 4.1.2.50
UniProt
Find proteins for Q7MR56 (Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / CCUG 13145 / JCM 31913 / LMG 7466 / NCTC 11488 / FDC 602W)) Explore Q7MR56  Go to UniProtKB:  Q7MR56

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.233 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.838	α = 90
b = 80.949	β = 113.24
c = 104.614	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
PHENIX	phasing
SOLVE	phasing
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-13 
Deposition Author(s): Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-10-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-11-27
  Changes: Data collection, Database references, Structure summary