4H0U | pdb_00004h0u

Crystal structure of thymidylate synthase from Corynebacterium glutamicum in complex with dUMP

• PDB DOI: https://doi.org/10.2210/pdb4H0U/pdb

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


• Deposited: 2012-09-10 Released: 2013-09-11 
• Deposition Author(s): Wang, W.C., Chang, C.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.241 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of thymidylate synthase from Corynebacterium glutamicum in complex with dUMP

Wang, W.C., Chang, C.M.

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: 122.28 kDa 
• Atom Count: 8,418 
• Modeled Residue Count: 1,026 
• Deposited Residue Count: 1,064 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase	A, B, C, D	266	Corynebacterium glutamicum ATCC 13032	Mutation(s): 0  Gene Names: cg0966, Cgl0844, thyA EC: 2.1.1.45
UniProt
Find proteins for Q8NS38 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q8NS38  Go to UniProtKB:  Q8NS38

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UMP	E [auth A], F [auth B], G [auth C], H [auth D]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C9 H13 N2 O8 P JSRLJPSBLDHEIO-SHYZEUOFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.241 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.042	α = 90
b = 87.815	β = 90
c = 165.747	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-11 
Deposition Author(s): Wang, W.C., Chang, C.M.

Revision History  

• Version 1.0: 2013-09-11
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description