3FNN | pdb_00003fnn

Biochemical and structural analysis of an atypical ThyX: Corynebacterium glutamicum NCHU 87078 depends on ThyA for thymidine biosynthesis

• PDB DOI: https://doi.org/10.2210/pdb3FNN/pdb

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


• Deposited: 2008-12-26 Released: 2009-12-29 
• Deposition Author(s): Wang, W.-C., Liu, J.-S., Chang, C.-M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.260 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

Biochemical and structural analysis of an atypical ThyX: Corynebacterium glutamicum NCHU 87078 depends on ThyA for thymidine biosynthesis

Wang, W.-C., Liu, J.-S., Chang, C.-M.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 29.71 kDa 
• Atom Count: 1,921 
• Modeled Residue Count: 227 
• Deposited Residue Count: 256 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase thyX	A	256	Corynebacterium glutamicum	Mutation(s): 0  EC: 2.1.1.148
UniProt
Find proteins for P40111 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore P40111  Go to UniProtKB:  P40111

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.260 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 4₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.806	α = 90
b = 95.806	β = 90
c = 64.637	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-29 
Deposition Author(s): Wang, W.-C., Liu, J.-S., Chang, C.-M.

Revision History  

• Version 1.0: 2009-12-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description