4NKP

Crystal structure of a putative extracellular heme-binding protein (DESPIG_02683) from Desulfovibrio piger ATCC 29098 at 1.24 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free: 0.149 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.129 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of a hypothetical protein (DESPIG_02683) from Desulfovibrio piger ATCC 29098 at 1.24 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
putative extracellular heme-binding proteinA, B, C, D148Desulfovibrio piger ATCC 29098Mutation(s): 0 
Gene Names: DESPIG_02683ZP_03312748.1
Find proteins for B6WX57 (Desulfovibrio piger ATCC 29098)
Explore B6WX57 
Go to UniProtKB:  B6WX57
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, B, C, D
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,B,C,DL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free: 0.149 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.129 
  • Space Group: P 4
  • Diffraction Data DOI: 10.18430/M34NKP Protein Diffraction
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.964α = 90
b = 80.964β = 90
c = 72.927γ = 90
Software Package:
Software NamePurpose
MolProbitymodel building
PDB_EXTRACTdata extraction
SOLVEphasing
XSCALEdata scaling
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-11
    Type: Initial release
  • Version 1.1: 2014-12-24
    Changes: Structure summary
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2018-01-24
    Changes: Database references