2NVM | pdb_00002nvm

Crystal structure of fdxN element excision controlling factor XisI (YP_321976.1) from Anabaena Variabilis ATCC 29413 at 2.19 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2NVM/pdb

• Classification: Structural Genomics/Unknown Function
• Organism(s): Trichormus variabilis ATCC 29413
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-11-13 Released: 2006-12-12 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 
  0.244 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.203 (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: 29.19 kDa 
• Atom Count: 1,851 
• Modelled Residue Count: 215 
• Deposited Residue Count: 252 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FdxN element excision controlling factor XisI	A, B	126	Trichormus variabilis ATCC 29413	Mutation(s): 0  Gene Names: YP_321976.1
UniProt
Find proteins for Q3MD55 (Trichormus variabilis (strain ATCC 29413 / PCC 7937)) Explore Q3MD55  Go to UniProtKB:  Q3MD55

Small Molecules

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: 2.19 Å
• R-Value Free:  0.244 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32NVM

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.44	α = 90
b = 122.44	β = 90
c = 77.076	γ = 120

Software Package:

Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-12 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2006-12-12
  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: 2024-10-30
  Changes: Data collection, Refinement description, Structure summary