6M4B | pdb_00006m4b

1510-N membrane-bound stomatin-specific protease S97A mutant

PDB DOI: https://doi.org/10.2210/pdb6M4B/pdb

Classification: HYDROLASE
Organism(s): Pyrococcus horikoshii OT3
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-03-06 Released: 2020-06-10
Deposition Author(s): Yokoyama, H., Suzuki, K.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.234 (Depositor), 0.240 (DCC)
R-Value Work:
0.192 (Depositor), 0.200 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Inactive dimeric structure of the protease domain of stomatin operon partner protein.

Yokoyama, H., Suzuki, K., Hara, K., Matsui, I., Hashimoto, H.

(2020) Acta Crystallogr D Biol Crystallogr 76: 515-520

DOI: https://doi.org/10.1107/S2059798320005021

Macromolecule Content

Total Structure Weight: 51.01 kDa
Atom Count: 3,239
Modeled Residue Count: 414
Deposited Residue Count: 460
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Membrane-bound protease PH1510	A, B	230	Pyrococcus horikoshii OT3	Mutation(s): 1 Gene Names: PH1510 EC: 3.4.21
UniProt
Find proteins for O59179 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O59179 Go to UniProtKB: O59179
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O59179
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 (Subject of Investigation/LOI) Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth B] MOL2 format, chain C [auth B] MOL2 format, chain D [auth B] mmCIF format, chain C [auth B] mmCIF format, chain D [auth B]	C [auth B], D [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth B] Focus chain D [auth B] Interactions & Density Focus chain C [auth B] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.234 (Depositor), 0.240 (DCC)
R-Value Work: 0.192 (Depositor), 0.200 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.731	α = 90
b = 124.731	β = 90
c = 56.545	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-06-10

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	17K07316

Revision History (Full details and data files)

Version 1.0: 2020-06-10
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Database references, Refinement description

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.