2OKF | pdb_00002okf

CRYSTAL STRUCTURE OF A FDXN ELEMENT EXCISION CONTROLLING FACTOR PROTEIN (AVA_3312) FROM ANABAENA VARIABILIS AT 1.60 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb2OKF/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Trichormus variabilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-01-16 Released: 2007-01-30 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.155 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.142 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.143 (Depositor) 

Literature

Site-specific recombination of nitrogen-fixation genes in cyanobacteria by XisF-XisH-XisI complex: Structures and models.

Hwang, W.C., Golden, J.W., Pascual, J., Xu, D., Cheltsov, A., Godzik, A.

(2014) Proteins 

• DOI: https://doi.org/10.1002/prot.24679

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: 32.72 kDa 
• Atom Count: 2,500 
• Modelled Residue Count: 258 
• Deposited Residue Count: 280 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FdxN element excision controlling factor protein	A, B	140	Trichormus variabilis	Mutation(s): 0  Gene Names: YP_323815.1, Ava_3312
UniProt
Find proteins for Q3M7W6 (Trichormus variabilis (strain ATCC 29413 / PCC 7937)) Explore Q3M7W6  Go to UniProtKB:  Q3M7W6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], M [auth B], N [auth B], O [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	D [auth A], E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	C [auth A], L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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: 1.60 Å
• R-Value Free:  0.155 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.142 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.143 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32OKF

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.81	α = 90
b = 59.81	β = 90
c = 73.19	γ = 120

Software Package:

Software Name	Purpose
MolProbity	model building
SOLVE	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-30 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-01-30
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2014-09-10
  Changes: Database references
• Version 1.4: 2014-09-24
  Changes: Database references
• Version 1.5: 2017-10-18
  Changes: Refinement description
• Version 1.6: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.7: 2024-11-20
  Changes: Data collection, Refinement description, Structure summary