2OHD | pdb_00002ohd

Crystal structure of hypothetical molybdenum cofactor biosynthesis protein C from Sulfolobus tokodaii

PDB DOI: https://doi.org/10.2210/pdb2OHD/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Sulfurisphaera tokodaii str. 7
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-01-10 Released: 2007-11-27
Deposition Author(s): Yoshida, H., Yamada, M., Kuramitsu, S., Kamitori, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.252 (Depositor), 0.250 (DCC)
R-Value Work:
0.202 (Depositor), 0.200 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structure of a putative molybdenum-cofactor biosynthesis protein C (MoaC) from Sulfolobus tokodaii (ST0472)

Yoshida, H., Yamada, M., Kuramitsu, S., Kamitori, S.

(2008) Acta Crystallogr Sect F Struct Biol Cryst Commun 64: 589-592

PubMed: 18607082 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S174430910801590X
Primary Citation of Related Structures:
2OHD

PubMed Abstract:
The crystal structure of a putative molybdenum-cofactor (Moco) biosynthesis protein C (MoaC) from Sulfolobus tokodaii (ST0472) was determined at 2.2 A resolution. The crystal belongs to the monoclinic space group C2, with unit-cell parameters a = 123.31, b = 78.58, c = 112.67 A, beta = 118.1 degrees . The structure was solved by molecular replacement using the structure of Escherichia coli MoaC as the probe model. The asymmetric unit is composed of a hexamer arranged as a trimer of dimers with noncrystallographic 32 symmetry. The structure of ST0472 is very similar to that of E. coli MoaC; however, in the ST0472 protein an additional loop formed by the insertion of seven residues participates in intermonomer interactions and the new structure also reveals the formation of an interdimer beta-sheet. These features may contribute to the stability of the oligomeric state.

Organizational Affiliation

Division of Structural Biology, Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan.

Macromolecule Content

Total Structure Weight: 102.91 kDa
Atom Count: 7,130
Modelled Residue Count: 846
Deposited Residue Count: 906
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable molybdenum cofactor biosynthesis protein C	A, B, C, D, E A, B, C, D, E, F	151	Sulfurisphaera tokodaii str. 7	Mutation(s): 0 Gene Names: ST0472 EC: 4.6.1.17
UniProt
Find proteins for Q975D5 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore Q975D5 Go to UniProtKB: Q975D5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q975D5
Sequence Annotations Expand
Reference Sequence LOADING

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.252 (Depositor), 0.250 (DCC)
R-Value Work: 0.202 (Depositor), 0.200 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.31	α = 90
b = 78.578	β = 118.06
c = 112.671	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-11-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-11-27
Type: Initial release
Version 1.1: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.2: 2023-10-25
Changes: Data collection, Database references, Refinement description