4GZ7 | pdb_00004gz7

The crystal structure of Apo-dihydropyrimidinase from Tetraodon nigroviridis

• PDB DOI: https://doi.org/10.2210/pdb4GZ7/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): Hsien, 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: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Literature

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

Hsien, 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: 55.62 kDa 
• Atom Count: 4,076 
• Modeled Residue Count: 492 
• Deposited Residue Count: 500 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dihydropyrimidinase	A	500	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
MHA	B [auth A], C [auth A], D [auth A]	(CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID C6 H10 N2 O5 QZTKDVCDBIDYMD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.195 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.823	α = 90
b = 160.823	β = 90
c = 94.547	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): Hsien, 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: 2024-03-20
  Changes: Data collection, Database references, Derived calculations