2P4G

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

• PDB DOI: https://doi.org/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)

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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 

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 30.48 kDa 
• Atom Count: 2,034 
• Modelled Residue Count: 248 
• Deposited Residue Count: 270 
• Unique protein chains: 1

Macromolecules

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
UniProt
Find proteins for Q6NGV8 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)) Explore Q6NGV8  Go to UniProtKB:  Q6NGV8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NO3	B [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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: https://doi.org/10.18430/M32P4G

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

Entry History 

Deposition Data

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

Revision History  

• 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
• Version 1.5: 2023-01-25
  Changes: Database references, Derived calculations