1O13 | pdb_00001o13

Crystal structure of a putative dinitrogenase iron-molybdenum cofactor (tm1816) from thermotoga maritima at 1.83 A resolution

PDB DOI: https://doi.org/10.2210/pdb1O13/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Thermotoga maritima
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2002-10-15 Released: 2002-12-18
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free:
0.241 (Depositor), 0.238 (DCC)
R-Value Work:
0.207 (Depositor), 0.206 (DCC)
R-Value Observed:
0.207 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1O13

This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of probable NifB protein that is involved in FeMo-Co biosynthesis TM1816 from Thermotoga maritima at 1.83 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 15.25 kDa
Atom Count: 904
Modeled Residue Count: 107
Deposited Residue Count: 136
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
probable NifB protein	A	136	Thermotoga maritima	Mutation(s): 2 Gene Names: TM1816
UniProt
Find proteins for Q9X2D6 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X2D6 Go to UniProtKB: Q9X2D6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9X2D6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free: 0.241 (Depositor), 0.238 (DCC)
R-Value Work: 0.207 (Depositor), 0.206 (DCC)
R-Value Observed: 0.207 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.57	α = 90
b = 39.84	β = 90
c = 85.77	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
RESOLVE	model building
SOLVE	phasing
CNS	refinement
CCP4	data scaling
RESOLVE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2002-12-18

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2002-12-18
Type: Initial release
Version 1.1: 2008-04-26
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-04
Changes: Advisory, Refinement description
Version 1.4: 2018-07-18
Changes: Data collection, Database references
Version 1.5: 2023-01-25
Changes: Advisory, Database references, Derived calculations
Version 1.6: 2024-11-20
Changes: Data collection, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.