8Y17 | pdb_00008y17

Crystal structure of a mutant Staphylococcus equorum manganese superoxide dismutase T89C and N187C

PDB DOI: https://doi.org/10.2210/pdb8Y17/pdb

Classification: OXIDOREDUCTASE
Organism(s): Staphylococcus equorum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-01-23 Released: 2025-01-29
Deposition Author(s): Putri, N.A., Fadillah, M.D., Yoshida, H., Retnoningrum, D.S., Artarini, A.A., Utami, R.A., Ismaya, W.T.
Funding Organization(s): Program Penelitian, Pengabdian kepada Masyarakat dan Inovasi ITB (P3MI-ITB) Grant Scheme 2023

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.276 (Depositor), 0.275 (DCC)
R-Value Work:
0.234 (Depositor), 0.236 (DCC)
R-Value Observed:
0.236 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8Y17

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of a mutant Staphylococcus equorum manganese superoxide dismutase T89C and N187C

Putri, N.A., Fadillah, M.D., Yoshida, H., Retnoningrum, D.S., Artarini, A.A., Utami, R.A., Ismaya, W.T.

To be published.

Macromolecule Content

Total Structure Weight: 94.19 kDa
Atom Count: 6,443
Modeled Residue Count: 793
Deposited Residue Count: 820
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase	A, B, C, D	205	Staphylococcus equorum	Mutation(s): 3 Gene Names: AST02_02815, M4L21_03170 EC: 1.15.1.1
UniProt
Find proteins for P0A0J3 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore P0A0J3 Go to UniProtKB: P0A0J3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A0J3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MN (Subject of Investigation/LOI) Query on MN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.276 (Depositor), 0.275 (DCC)
R-Value Work: 0.234 (Depositor), 0.236 (DCC)
R-Value Observed: 0.236 (Depositor)

Diffraction Data:

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 156.92	α = 90
b = 135.82	β = 102.74
c = 76.38	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-01-29

Deposition Author(s):

Retnoningrum, D.S.

Funding Organization	Location	Grant Number
Program Penelitian, Pengabdian kepada Masyarakat dan Inovasi ITB (P3MI-ITB) Grant Scheme 2023	Indonesia	56/IT1/C10/SK-KU/2023

Revision History (Full details and data files)

Version 1.0: 2025-01-29
Type: Initial release

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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.