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.

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)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	H3C542
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX Query on 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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-09-11

Deposition Author(s):

Revision History (Full details and data files)

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

Prepare Data

Validate Data

Deposit Data

Help and Resources

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The crystal structure of di-Zn dihydropyrimidinase from Tetraodon nigroviridis

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

4H01 | pdb_00004h01