3KTD | pdb_00003ktd

CRYSTAL STRUCTURE OF A PUTATIVE PREPHENATE DEHYDROGENASE (CGL0226) FROM CORYNEBACTERIUM GLUTAMICUM ATCC 13032 AT 2.60 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb3KTD/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Corynebacterium glutamicum ATCC 13032
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-11-24 Released: 2010-02-02 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.254 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Literature

Crystal structure of Prephenate dehydrogenase (NP_599479.1) from CORYNEBACTERIUM GLUTAMICUM ATCC 13032 KITASATO at 2.60 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 (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 147.05 kDa 
• Atom Count: 9,588 
• Modeled Residue Count: 1,281 
• Deposited Residue Count: 1,364 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prephenate dehydrogenase	A, B, C, D	341	Corynebacterium glutamicum ATCC 13032	Mutation(s): 0  Gene Names: Cgl0226
UniProt
Find proteins for Q8NTS6 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q8NTS6  Go to UniProtKB:  Q8NTS6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	F [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.254 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33KTD

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.322	α = 90
b = 107.23	β = 90
c = 146.915	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-02 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2010-02-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-27
  Changes: Data collection, Refinement description, Structure summary