Macromolecule Content

Total Structure Weight: 95.07 kDa
Atom Count: 7,411
Modelled Residue Count: 798
Deposited Residue Count: 820
Unique protein chains: 1

7WNK

Crystal structure of a mutant Staphylococcus equorum manganese superoxide dismutase K38R and A121E

PDB DOI: 10.2210/pdb7WNK/pdb

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

Deposited: 2022-01-18 Released: 2023-01-25
Deposition Author(s): Retnoningrum, D.S., Yoshida, H., Artarini, A.A., Ismaya, W.T.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.194
R-Value Work: 0.178
R-Value Observed: 0.179

wwPDB Validation 3D Report Full Report

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

Literature

Introducing intermolecular interaction to strengthen the stability of MnSOD dimer

Retnoningrum, D.S., Yoshida, H., Pajatiwi, I., Muliadi, R., Utami, R.A., Artarini, A., Ismaya, W.T.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 EC: 1.15.1.1
UniProt
Find proteins for A0A1E5TT85 (Staphylococcus equorum) Explore A0A1E5TT85 Go to UniProtKB: A0A1E5TT85
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1E5TT85
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain P [auth D] MOL2 format, chain F [auth A] MOL2 format, chain P [auth D]	F [auth A], P [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Ligand Interaction
BR Query on BR Download Ideal Coordinates CCD File SDF format, chain O [auth D] MOL2 format, chain O [auth D]	O [auth D]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Ligand Interaction
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D]	E [auth A], H [auth B], K [auth C], M [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Ligand Interaction
AZI Query on AZI Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] MOL2 format, chain G [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D]	G [auth B], I [auth B], J [auth B], L [auth C], N [auth D]	AZIDE ION N₃ IVRMZWNICZWHMI-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.194
R-Value Work: 0.178
R-Value Observed: 0.179
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.765	α = 90
b = 113.174	β = 90
c = 119.908	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-01-25

Deposition Author(s):

Retnoningrum, D.S.

Funding Organization	Location	Grant Number
Other government	Indonesia	079/E4.1/AK.04.PT/2021

Revision History (Full details and data files)

Version 1.0: 2023-01-25
Type: Initial release
Version 1.1: 2023-02-01
Changes: Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.