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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free:
0.244 (Depositor), 0.283 (DCC)
R-Value Work:
0.201 (Depositor)
R-Value Observed:
0.203 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2NVM

This is version 1.7 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 29.19 kDa
Atom Count: 1,851
Modeled Residue Count: 215
Deposited Residue Count: 252
Unique protein chains: 1

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3MD55
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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), 0.283 (DCC)
R-Value Work: 0.201 (Depositor)
R-Value Observed: 0.203 (Depositor)

Diffraction Data:

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

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Entry History

Deposition Data

Released Date: 2006-12-12

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.