4LG3

Crystal structure of a DUF487 family protein (DESPIG_00776) from Desulfovibrio piger ATCC 29098 at 2.49 A resolution

• PDB DOI:  https://doi.org/10.2210/pdb4LG3/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Desulfovibrio piger ATCC 29098
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-06-27 Released: 2013-08-21 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.225 
• R-Value Work: 0.180 
• R-Value Observed: 0.183 

Literature

Crystal structure of a hypothetical protein (DESPIG_00776) from Desulfovibrio piger ATCC 29098 at 2.49 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 62.31 kDa 
• Atom Count: 4,608 
• Modelled Residue Count: 539 
• Deposited Residue Count: 549 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C	183	Desulfovibrio piger ATCC 29098	Mutation(s): 0  Gene Names: DESPIG_00776
UniProt
Find proteins for B6WRT5 (Desulfovibrio piger ATCC 29098) Explore B6WRT5  Go to UniProtKB:  B6WRT5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], F [auth A], I [auth B], K [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	G [auth A], H [auth A], J [auth B], L [auth C], M [auth C], N [auth C], O [auth C], P [auth C], Q [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.225 
• R-Value Work: 0.180 
• R-Value Observed: 0.183 
• Space Group: P 3₂ 2 1
• Diffraction Data: https://doi.org/10.18430/M34LG3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.413	α = 90
b = 85.413	β = 90
c = 197.896	γ = 120

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
BUSTER-TNT	refinement
XDS	data reduction
SHELXD	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-21 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2013-08-21
  Type: Initial release
  
• Version 1.1: 2014-12-24
  Changes: Structure summary
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2023-02-01
  Changes: Database references, Derived calculations