3K6H | pdb_00003k6h

Crystal structure of a nitroreductase family protein from Agrobacterium tumefaciens str. C58

• PDB DOI: https://doi.org/10.2210/pdb3K6H/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2009-10-08 Released: 2009-10-27 
• Deposition Author(s): Tan, K., Xu, X., Cui, H., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free: 
  0.247 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

Crystal structure of a nitroreductase family protein from Agrobacterium tumefaciens str. C58

Tan, K., Xu, X., Cui, H., Savchenko, A., Edwards, A., Joachimiak, A.

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: 45.75 kDa 
• Atom Count: 3,103 
• Modeled Residue Count: 382 
• Deposited Residue Count: 394 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitroreductase family protein	A, B	197	Agrobacterium fabrum str. C58	Mutation(s): 0  Gene Names: AGR_C_3200, Atu1744 EC: 1
UniProt
Find proteins for A9CIP6 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CIP6  Go to UniProtKB:  A9CIP6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	F [auth A], K [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
SO4	C [auth A], D [auth A], E [auth A], G [auth B], H [auth B], I [auth B], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free:  0.247 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.47	α = 90
b = 127.47	β = 90
c = 150.983	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
RESOLVE	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-27 
Deposition Author(s): Tan, K., Xu, X., Cui, H., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-10-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary