1mmm

DISTINCT METAL ENVIRONMENT IN IRON-SUBSTITUTED MANGANESE SUPEROXIDE DISMUTASE PROVIDES A STRUCTURAL BASIS OF METAL SPECIFICITY

Method: X-RAY DIFFRACTION Dmax: 77.0 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (IRON-SUBSTITUTED MANGANESE SUPEROXIDE DISMUTASE)

OrganismNot specified

UniProt P00448

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–205 Chain B; UniProt 1–205 Not recorded OH HYDROXIDE ION × 3 FE FE (III) ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8.75;pH 8.75 Resolution 2.20 Å R-free 0.231

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

12 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SODM_ECOLI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–205; UniProt 1–205 Author chain B; PDBConstruct 1–205; UniProt 1–205

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1mmm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1mmm
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1mmm
Deposition date deposition_date1998-08-26
Structure title titleDISTINCT METAL ENVIRONMENT IN IRON-SUBSTITUTED MANGANESE SUPEROXIDE DISMUTASE PROVIDES A STRUCTURAL BASIS OF METAL SPECIFICITY
Keywords keywordsIRON-SUBSTITUTED MANGANESE SUPEROXIDE DISMUTASE, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier22.91
Radius of gyration Rg (electron density) rg_electron22.17
Forward intensity I(0) i035131200.00
Molecular weight molecular_weight46091.0 kDa
Excluded volume excluded_volume57752 ų
Envelope volume envelope_volume66386 ų
Hydration-shell volume shell_volume24713 ų
Envelope diameter envelope_diameter76.3
Shell Rg shell_rg29.38
Envelope Rg envelope_rg22.46
Shape Rg shape_rg22.13
Total Rg total_rg23.15
Total atoms total_atoms3261
Residues n_residues410
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax77.0
Rg (real space) rg_real22.85
Rg uncertainty (real space) rg_real_error0.47
I(0) (real space) i0_real3.5130e+07
I(0) uncertainty (real space) i0_real_error4.3660e+05
Rg (reciprocal space) rg_reciprocal22.87
I(0) (reciprocal space) i0_reciprocal35130000.0000
Solution quality estimate total_estimate0.8813
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.1
Skewness Skewness skewness0.307
Kurtosis Kurtosis kurtosis-0.282
Angular range angular_range— – 0.3450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12420000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.821; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.995

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1mmma1
Class classa — All alpha proteins
Fold Fold folda.2 — Long alpha-hairpin
Superfamily Superfamily superfamilya.2.11 — Fe,Mn superoxide dismutase (SOD), N-terminal domain
Family Family familya.2.11.1 — Fe,Mn superoxide dismutase (SOD), N-terminal domain
Domain ID domain_idd1mmma2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.44 — Fe,Mn superoxide dismutase (SOD), C-terminal domain
Superfamily Superfamily superfamilyd.44.1 — Fe,Mn superoxide dismutase (SOD), C-terminal domain
Family Family familyd.44.1.1 — Fe,Mn superoxide dismutase (SOD), C-terminal domain
Domain ID domain_idd1mmmb1
Class classa — All alpha proteins
Fold Fold folda.2 — Long alpha-hairpin
Superfamily Superfamily superfamilya.2.11 — Fe,Mn superoxide dismutase (SOD), N-terminal domain
Family Family familya.2.11.1 — Fe,Mn superoxide dismutase (SOD), N-terminal domain
Domain ID domain_idd1mmmb2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.44 — Fe,Mn superoxide dismutase (SOD), C-terminal domain
Superfamily Superfamily superfamilyd.44.1 — Fe,Mn superoxide dismutase (SOD), C-terminal domain
Family Family familyd.44.1.1 — Fe,Mn superoxide dismutase (SOD), C-terminal domain

CATH v4.4 (4 domains)

Domain ID domain_id1mmmA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily990 — Fe,Mn superoxide dismutase (SOD) domain
Domain ID domain_id1mmmA02
Class class3 — Alpha Beta
Architecture architecture55 — 3-Layer(bab) Sandwich
Topology topology40 — minor pseudopilin epsh fold
Homologous superfamily homologous superfamily20 — Iron/manganese superoxide dismutase, C-terminal domain
Domain ID domain_id1mmmB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily990 — Fe,Mn superoxide dismutase (SOD) domain
Domain ID domain_id1mmmB02
Class class3 — Alpha Beta
Architecture architecture55 — 3-Layer(bab) Sandwich
Topology topology40 — minor pseudopilin epsh fold
Homologous superfamily homologous superfamily20 — Iron/manganese superoxide dismutase, C-terminal domain

8. Citations (1)

9. Files and Curves (10)