3LSU | pdb_00003lsu

Crystal Structure of SOD2 from Saccharomyces cerevisiae

PDB DOI: https://doi.org/10.2210/pdb3LSU/pdb

Classification: OXIDOREDUCTASE
Organism(s): Saccharomyces cerevisiae
Expression System: Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2010-02-12 Released: 2011-02-23
Deposition Author(s): Sheng, Y., Cascio, D., Valentine, J.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.195 (Depositor), 0.190 (DCC)
R-Value Work:
0.162 (Depositor), 0.160 (DCC)
R-Value Observed:
0.163 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of SOD2 from Saccharomyces cerevisiae

Sheng, Y., Cascio, D., Valentine, J.S.

To be published.

Macromolecule Content

Total Structure Weight: 94.77 kDa
Atom Count: 7,111
Modeled Residue Count: 826
Deposited Residue Count: 828
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Mn], mitochondrial	A, B, C, D	207	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: SOD2, YHR008C EC: 1.15.1.1
UniProt
Find proteins for P00447 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00447 Go to UniProtKB: P00447
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00447
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] SDF format, chain M [auth D] MOL2 format, chain G [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] MOL2 format, chain M [auth D] mmCIF format, chain G [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D] mmCIF format, chain M [auth D]	G [auth B], J [auth C], L [auth D], M [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D] Focus chain M [auth D] Interactions & Density Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D] Focus chain M [auth D]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain H [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain H [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain H [auth C] mmCIF format, chain K [auth D]	E [auth A], F [auth B], H [auth C], K [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain H [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain H [auth C] Focus chain K [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain I [auth C] MOL2 format, chain I [auth C] mmCIF format, chain I [auth C]	I [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Interactions & Density Focus chain I [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY Query on MLY	A, B, C, D	L-PEPTIDE LINKING	C₈ H₁₈ N₂ O₂		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.195 (Depositor), 0.190 (DCC)
R-Value Work: 0.162 (Depositor), 0.160 (DCC)
R-Value Observed: 0.163 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.657	α = 109.36
b = 64.933	β = 106.35
c = 66.55	γ = 109.68

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-02-23

Deposition Author(s):

Sheng, Y.

Cascio, D.

Valentine, J.S.

Revision History (Full details and data files)

Version 1.0: 2011-02-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description

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Crystal Structure of SOD2 from Saccharomyces cerevisiae

Crystal Structure of SOD2 from Saccharomyces cerevisiae

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

3LSU | pdb_00003lsu