3D7N | pdb_00003d7n

The crystal structure of the flavodoxin, WrbA-like protein from Agrobacterium tumefaciens

• PDB DOI: https://doi.org/10.2210/pdb3D7N/pdb

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


• Deposited: 2008-05-21 Released: 2008-07-15 
• Deposition Author(s): Zhang, R., Xu, X., Gu, J., Savchenko, A., Edwards, 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: 
  0.254 (Depositor), 0.308 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.275 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Literature

The crystal structure of the flavodoxin, WrbA-like protein from Agrobacterium tumefaciens

Zhang, R., Xu, X., Gu, J., Savchenko, A., Edwards, A., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 20.94 kDa 
• Atom Count: 1,214 
• Modeled Residue Count: 157 
• Deposited Residue Count: 193 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flavodoxin, WrbA-like protein	A	193	Agrobacterium fabrum str. C58	Mutation(s): 0  Gene Names: AGR_L_1309, Atu4201
UniProt
Find proteins for A9CG77 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CG77  Go to UniProtKB:  A9CG77

Small Molecules

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:  0.254 (Depositor), 0.308 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.275 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.948	α = 90
b = 73.948	β = 90
c = 144.488	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-15 
Deposition Author(s): Zhang, R., Xu, X., Gu, J., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-07-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary