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

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:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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

View Full Validation Report

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

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.