Macromolecule Content

Total Structure Weight: 30.48 kDa
Atom Count: 2034
Modelled Residue Count: 248
Deposited Residue Count: 270
Unique protein chains: 1

2P4G

CRYSTAL STRUCTURE OF A PYRIMIDINE REDUCTASE-LIKE PROTEIN (DIP1392) FROM CORYNEBACTERIUM DIPHTHERIAE NCTC AT 2.30 A RESOLUTION

DOI: 10.2210/pdb2P4G/pdb

Classification: OXIDOREDUCTASE
Organism(s): Corynebacterium diphtheriae NCTC 13129
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-03-12 Released: 2007-03-27
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.225
R-Value Work: 0.173
R-Value Observed: 0.175

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of hypothetical protein (NP_939744.1) from Corynebacterium diphtheriae at 2.30 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein	A	270	Corynebacterium diphtheriae NCTC 13129	Mutation(s): 4 Gene Names: NP_939744.1, DIP1392
Find proteins for Q6NGV8 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)) Explore Q6NGV8 Go to UniProtKB: Q6NGV8
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [A] SDF format, chain D [A] SDF format, chain E [A] SDF format, chain F [A] SDF format, chain G [A] SDF format, chain H [A] SDF format, chain I [A] SDF format, chain J [A] SDF format, chain K [A] SDF format, chain L [A] SDF format, chain M [A] SDF format, chain N [A] SDF format, chain O [A] SDF format, chain P [A] SDF format, chain Q [A] MOL2 format, chain C [A] MOL2 format, chain D [A] MOL2 format, chain E [A] MOL2 format, chain F [A] MOL2 format, chain G [A] MOL2 format, chain H [A] MOL2 format, chain I [A] MOL2 format, chain J [A] MOL2 format, chain K [A] MOL2 format, chain L [A] MOL2 format, chain M [A] MOL2 format, chain N [A] MOL2 format, chain O [A] MOL2 format, chain P [A] MOL2 format, chain Q [A]	A	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Ligand Interaction
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain B [A] MOL2 format, chain B [A]	A	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Ligand Interaction

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: 2.30 Å
R-Value Free: 0.225
R-Value Work: 0.173
R-Value Observed: 0.175
Space Group: P 6₄
Diffraction Data DOI: 10.18430/M32P4G Protein Diffraction

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.51	α = 90
b = 113.51	β = 90
c = 55.94	γ = 120

Software Package:

Software Name	Purpose
MolProbity	model building
SOLVE	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2007-03-12
Released Date: 2007-03-27

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2007-03-27
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2017-10-25
Changes: Author supporting evidence

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Deposition Help & Resources

177426 Biological Macromolecular Structures Enabling Breakthroughs in Research and Education