3VTG | pdb_00003vtg

High choriolytic enzyme 1 (HCE-1), a hatching enzyme zinc-protease from Oryzias latipes (Medaka fish)

PDB DOI: https://doi.org/10.2210/pdb3VTG/pdb

Classification: HYDROLASE
Organism(s): Oryzias latipes
Mutation(s): No

Deposited: 2012-05-30 Released: 2013-06-05
Deposition Author(s): Kudo, N., Yasumasu, S., Iuchi, I., Tanokura, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.34 Å
R-Value Free:
0.204 (Depositor), 0.203 (DCC)
R-Value Work:
0.187 (Depositor), 0.186 (DCC)
R-Value Observed:
0.188 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3VTG

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of High choriolytic enzyme 1 (HCE-1), a hatching enzyme from Oryzias latipes (Medaka fish)

Kudo, N., Yasumasu, S., Iuchi, I., Tanokura, M.

To be published.

Macromolecule Content

Total Structure Weight: 22.78 kDa
Atom Count: 1,889
Modeled Residue Count: 200
Deposited Residue Count: 200
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
High choriolytic enzyme 1	A	200	Oryzias latipes	Mutation(s): 0 EC: 3.4.24.67
UniProt
Find proteins for P31580 (Oryzias latipes) Explore P31580 Go to UniProtKB: P31580
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P31580
Sequence Annotations Expand
Reference Sequence

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] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.34 Å
R-Value Free: 0.204 (Depositor), 0.203 (DCC)
R-Value Work: 0.187 (Depositor), 0.186 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.006	α = 90
b = 30.461	β = 123.69
c = 79.653	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-06-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-06-05
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.