4M1F | pdb_00004m1f

X-ray crystal structure of E. coli apo NrdF

• PDB DOI: https://doi.org/10.2210/pdb4M1F/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-08-02 Released: 2013-08-28 
• Deposition Author(s): Boal, A.K., Cotruvo Jr., J.A., Stubbe, J., Rosenzweig, A.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.199 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

X-ray crystal structure of E. coli apo NrdF

Boal, A.K., Cotruvo Jr., J.A., Stubbe, J., Rosenzweig, A.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 36.48 kDa 
• Atom Count: 2,539 
• Modelled Residue Count: 284 
• Deposited Residue Count: 319 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonucleoside-diphosphate reductase 2 subunit beta	A	319	Escherichia coli K-12	Mutation(s): 0  Gene Names: b2676, JW2651, nrdF, ygaD EC: 1.17.4.1
UniProt
Find proteins for P37146 (Escherichia coli (strain K12)) Explore P37146  Go to UniProtKB:  P37146

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.199 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.511	α = 90
b = 78.511	β = 90
c = 267.294	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-28 
Deposition Author(s): Boal, A.K., Cotruvo Jr., J.A., Stubbe, J., Rosenzweig, A.C.

Revision History  

• Version 1.0: 2013-08-28
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Refinement description