3QVO | pdb_00003qvo

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

• PDB DOI: https://doi.org/10.2210/pdb3QVO/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Shigella flexneri 2a str. 2457T
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-02-25 Released: 2011-06-01 
• Deposition Author(s): Cuff, M.E., Xu, X., Cui, H., Edwards, A., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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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) 

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.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 26.62 kDa 
• Atom Count: 1,607 
• Modeled Residue Count: 197 
• Deposited Residue Count: 236 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NmrA family protein	A	236	Shigella flexneri 2a str. 2457T	Mutation(s): 0  Gene Names: S1416, SF2457T_2192

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MNB	B [auth A]	5-MERCAPTO-2-NITRO-BENZOIC ACID C7 H5 N O4 S GANZODCWZFAEGN-UHFFFAOYSA-N

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

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 = 73.524	α = 90
b = 73.524	β = 90
c = 130.246	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-01 
Deposition Author(s): Cuff, M.E., Xu, X., Cui, H., Edwards, A., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• 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