4H01 | pdb_00004h01

The crystal structure of di-Zn dihydropyrimidinase from Tetraodon nigroviridis

• PDB DOI: https://doi.org/10.2210/pdb4H01/pdb

• Classification: HYDROLASE
• Organism(s): Tetraodon nigroviridis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-09-06 Released: 2013-09-11 
• Deposition Author(s): Hsieh, Y.C., Chen, M.C., Hsu, C.C., Chan, S.I., Yang, Y.S., Chen, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Literature

Lysine Carboxylation: Metal and Structural Requirements for Post-translational Modification

Hsieh, Y.C., Chen, M.C., Hsu, C.C., Chan, S.I., Yang, Y.S., Chen, C.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 57.06 kDa 
• Atom Count: 3,977 
• Modeled Residue Count: 485 
• Deposited Residue Count: 520 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dihydropyrimidinase	A	520	Tetraodon nigroviridis	Mutation(s): 0  Gene Names: DPYS
UniProt
Find proteins for H3C542 (Tetraodon nigroviridis) Explore H3C542  Go to UniProtKB:  H3C542

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.478	α = 90
b = 160.478	β = 90
c = 93.296	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): Hsieh, Y.C., Chen, M.C., Hsu, C.C., Chan, S.I., Yang, Y.S., Chen, C.J.

Revision History  

• Version 1.0: 2013-09-11
  Type: Initial release
  
• Version 1.1: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary