3D82

Crystal structure of a cupin-2 domain containing protein (sfri_3543) from shewanella frigidimarina ncimb 400 at 2.05 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of Domain of Unknown Function with a Cupin Fold (YP_752209.1) from SHEWANELLA FRIGIDIMARINA NCIMB 400 at 2.05 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cupin 2, conserved barrel domain protein
A, B, C, D, E
102Shewanella frigidimarina (strain NCIMB 400)Mutation(s): 0 
Find proteins for Q07X94 (Shewanella frigidimarina (strain NCIMB 400))
Go to UniProtKB:  Q07X94
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
D, E
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
A, B, C, D, E
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 56.920α = 90.00
b = 95.140β = 90.00
c = 237.370γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
autoSHARPphasing
SHELXphasing
PHENIXrefinement
XDSdata reduction
MolProbitymodel building
SHELXDphasing
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-06-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Author supporting evidence, Refinement description
  • Version 1.3: 2019-07-24
    Type: Data collection, Derived calculations, Refinement description