3QVO | pdb_00003qvo

Structure of a Rossmann-fold NAD(P)-binding family protein from Shigella flexneri.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.251 (Depositor), 0.243 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


Literature

Structure of a Rossmann-fold NAD(P)-binding family protein from Shigella flexneri.

Cuff, M.E., Xu, X., Cui, H., Edwards, A., Savchenko, A., Joachimiak, A.

To be published.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NmrA family protein236Shigella flexneri 2a str. 2457TMutation(s): 0 
Gene Names: S1416, SF2457T_2192
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MNB
Query on MNB
Download Ideal Coordinates CCD File 
B [auth A]5-MERCAPTO-2-NITRO-BENZOIC ACID
C7 H5 N O4 S
GANZODCWZFAEGN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.251 (Depositor), 0.243 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.524α = 90
b = 73.524β = 90
c = 130.246γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MLPHAREphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-10-03
    Changes: Data collection
  • Version 1.3: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Structure summary