3AH7 | pdb_00003ah7

Crystal structure of the ISC-like [2Fe-2S] ferredoxin (FdxB) from Pseudomonas putida JCM 20004

• PDB DOI: https://doi.org/10.2210/pdb3AH7/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Pseudomonas putida
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-04-20 Released: 2011-04-20 
• Deposition Author(s): Kumasaka, T., Shimizu, N., Ohmori, D., Iwasaki, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.216 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the ISC-like [2Fe-2S] ferredoxin (FdxB) from Pseudomonas putida JCM 20004

Iwasaki, T., Kappl, R., Bracic, G., Shimizu, N., Ohmori, D., Kumasaka, T.

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: 12.75 kDa 
• Atom Count: 1,019 
• Modeled Residue Count: 109 
• Deposited Residue Count: 113 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
[2Fe-2S]ferredoxin	A	113	Pseudomonas putida	Mutation(s): 0  Gene Names: fdxB
UniProt
Find proteins for Q76CS9 (Pseudomonas putida) Explore Q76CS9  Go to UniProtKB:  Q76CS9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FES	B [auth A]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.216 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.575	α = 90
b = 87.575	β = 90
c = 73.139	γ = 120

Software Package:

Software Name	Purpose
BSS	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-20 
Deposition Author(s): Kumasaka, T., Shimizu, N., Ohmori, D., Iwasaki, T.

Revision History  

• Version 1.0: 2011-04-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description