3SFW | pdb_00003sfw

Crystal structure of dihydropyrimidinase from Brevibacillus agri NCHU1002

• PDB DOI: https://doi.org/10.2210/pdb3SFW/pdb

• Classification: HYDROLASE
• Organism(s): Brevibacillus agri
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-06-14 Released: 2012-06-20 
• Deposition Author(s): Wang, W.C., Wu, H.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 
  0.190 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.147 (Depositor), 0.147 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of dihydropyrimidinase from Brevibacillus agri NCHU1002

Wang, W.C., Wu, H.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: 101.78 kDa 
• Atom Count: 8,276 
• Modeled Residue Count: 922 
• Deposited Residue Count: 922 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydropyrimidinase	A, B	461	Brevibacillus agri	Mutation(s): 0  Gene Names: pydB EC: 3.5.2.2
UniProt
Find proteins for Q846U5 (Brevibacillus agri) Explore Q846U5  Go to UniProtKB:  Q846U5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A], F [auth A], H [auth B], I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	C [auth A], E [auth A], G [auth A], J [auth B], K [auth B], L [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free:  0.190 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.147 (Depositor), 0.147 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.807	α = 90
b = 109.112	β = 90
c = 140.984	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-20 
Deposition Author(s): Wang, W.C., Wu, H.M.

Revision History  

• Version 1.0: 2012-06-20
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-12-06
  Changes: Data collection