5GSL | pdb_00005gsl

Glycoside hydrolase A

PDB DOI: https://doi.org/10.2210/pdb5GSL/pdb

Classification: HYDROLASE
Organism(s): Pyrococcus horikoshii OT3
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-08-16 Released: 2017-02-01
Deposition Author(s): Watanabe, M., Kamachi, S., Mine, S.
Funding Organization(s): The Japan Society for the Promotion of Sciences

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.288 (Depositor), 0.282 (DCC)
R-Value Work:
0.217 (Depositor), 0.218 (DCC)
R-Value Observed:
0.221 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5GSL

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

Literature

Glycoside hydrolase A

Watanabe, M., Kamachi, S., Mine, S.

To be published.

Macromolecule Content

Total Structure Weight: 182.85 kDa
Atom Count: 13,033
Modeled Residue Count: 1,550
Deposited Residue Count: 1,556
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
778aa long hypothetical beta-galactosidase	A, B	778	Pyrococcus horikoshii OT3	Mutation(s): 0 Gene Names: PH0511 EC: 3.2.1
UniProt
Find proteins for O58247 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58247 Go to UniProtKB: O58247
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O58247
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B]	C [auth A], D [auth A], E [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.288 (Depositor), 0.282 (DCC)
R-Value Work: 0.217 (Depositor), 0.218 (DCC)
R-Value Observed: 0.221 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.843	α = 90
b = 148.767	β = 90
c = 165.69	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-02-01

Deposition Author(s):

Funding Organization	Location	Grant Number
The Japan Society for the Promotion of Sciences	Japan	25450143

Revision History (Full details and data files)

Version 1.0: 2017-02-01
Type: Initial release
Version 1.1: 2020-02-26
Changes: Data collection
Version 1.2: 2024-03-20
Changes: Data collection, Database references

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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.