4TQT

Crystal structure of Dihydropyrimidinase from Brucella suis

• PDB DOI: https://doi.org/10.2210/pdb4TQT/pdb

• Classification: HYDROLASE
• Organism(s): Brucella suis 1330
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-06-12 Released: 2014-08-06 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.182 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.135 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.137 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Dihydropyrimidinase from Brucella suis

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Abendroth, J., Davies, D.R., Lorimer, D., Edwards, T.E.

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)

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 330.78 kDa 
• Atom Count: 23,274 
• Modelled Residue Count: 2,869 
• Deposited Residue Count: 2,982 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-hydantoinase	A, B, C, D, E, F	497	Brucella suis 1330	Mutation(s): 0  Gene Names: dhT, BR0278, BS1330_I0279 EC: 3.5.2.2
UniProt
Find proteins for A0A0H3G9X2 (Brucella suis biovar 1 (strain 1330)) Explore A0A0H3G9X2  Go to UniProtKB:  A0A0H3G9X2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	EA [auth E], FA [auth E], G [auth A], H [auth A], KA [auth F], LA [auth F], N [auth B], O [auth B], S [auth C], T [auth C], Y [auth D], Z [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	AA [auth D], BA [auth D], CA [auth D], DA [auth D], GA [auth E], HA [auth E], I [auth A], IA [auth E], J [auth A], JA [auth E], K [auth A], L [auth A], M [auth A], MA [auth F], NA [auth F], OA [auth F], P [auth B], PA [auth F], Q [auth B], R [auth B], U [auth C], V [auth C], W [auth C], X [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A, B, C, D, E, F	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.182 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.135 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.137 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34TQT

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 156.69	α = 90
b = 88.83	β = 91.17
c = 221.24	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
ARP	model building
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-08-06 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2014-08-06
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Database references, Derived calculations, Other, Refinement description, Source and taxonomy
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection