2G2C | pdb_00002g2c

Putative molybdenum cofactor biosynthesis protein from Corynebacterium diphtheriae.

PDB DOI: https://doi.org/10.2210/pdb2G2C/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Corynebacterium diphtheriae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2006-02-15 Released: 2006-03-28
Deposition Author(s): Osipiuk, J., Li, H., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.202 (Depositor), 0.172 (DCC)
R-Value Work:
0.171 (Depositor), 0.172 (DCC)
R-Value Observed:
0.174 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

Literature

X-ray crystal structure of putative molybdenum cofactor biosynthesis protein from Corynebacterium diphtheriae.

Osipiuk, J., Li, H., Clancy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 17.84 kDa
Atom Count: 1,401
Modeled Residue Count: 152
Deposited Residue Count: 167
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative molybdenum cofactor biosynthesis protein	A	167	Corynebacterium diphtheriae	Mutation(s): 2 Gene Names: DIP0503
UniProt
Find proteins for Q6NJA6 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)) Explore Q6NJA6 Go to UniProtKB: Q6NJA6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6NJA6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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: 1.50 Å
R-Value Free: 0.202 (Depositor), 0.172 (DCC)
R-Value Work: 0.171 (Depositor), 0.172 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.822	α = 90
b = 67.822	β = 90
c = 114.276	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
SCALEPACK	data scaling
HKL-3000	phasing
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-03-28

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2006-03-28
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Derived calculations, 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.