3wyo

Heterodimeric myoglobin formed by domain swapping

Method: X-RAY DIFFRACTION Dmax: 97.0 Å Quality: GOOD

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

Myoglobin

Equus caballus

UniProt P68082

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 2–154 Chain B; UniProt 2–154 Mutation:H64V/V68H/E85K/D141K Mutation:K78E/K79D HEM PROTOPORPHYRIN IX CONTAINING FE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;277 K;25% (w/v) PEG 1000, 100mM MES-NaOH buffer, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.00 Å R-free 0.266
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 2–154 Chain D; UniProt 2–154 Mutation:H64V/V68H/E85K/D141K Mutation:K78E/K79D HEM PROTOPORPHYRIN IX CONTAINING FE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;277 K;25% (w/v) PEG 1000, 100mM MES-NaOH buffer, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.00 Å R-free 0.266

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.

149 other PDB entries and 155 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MYG_HORSE
Isoform
PDB entities 1, 2
Chains and sequence ranges Author chain A; PDBConstruct 1–153; UniProt 2–154 Author chain C; PDBConstruct 1–153; UniProt 2–154 Author chain B; PDBConstruct 1–153; UniProt 2–154 Author chain D; PDBConstruct 1–153; UniProt 2–154

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 3wyo

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3wyo
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3wyo
Deposition date deposition_date2014-09-04
Structure title titleHeterodimeric myoglobin formed by domain swapping
Keywords keywordsGlobin, Oxygen Binding; OXYGEN BINDING
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier29.36
Radius of gyration Rg (electron density) rg_electron28.59
Forward intensity I(0) i074398500.00
Molecular weight molecular_weight70272.0 kDa
Excluded volume excluded_volume89024 ų
Envelope volume envelope_volume111900 ų
Hydration-shell volume shell_volume33375 ų
Envelope diameter envelope_diameter105.7
Shell Rg shell_rg35.33
Envelope Rg envelope_rg28.06
Shape Rg shape_rg28.57
Total Rg total_rg29.33
Total atoms total_atoms4968
Residues n_residues612
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 dmax97.0
Rg (real space) rg_real29.34
Rg uncertainty (real space) rg_real_error0.68
I(0) (real space) i0_real7.4400e+07
I(0) uncertainty (real space) i0_real_error1.1130e+06
Rg (reciprocal space) rg_reciprocal29.35
I(0) (reciprocal space) i0_reciprocal74400000.0000
Solution quality estimate total_estimate0.8932
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.9
Skewness Skewness skewness0.330
Kurtosis Kurtosis kurtosis-0.267
Angular range angular_range— – 0.2700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10970000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.880; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.969

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3wyoa_
Class classa — All alpha proteins
Fold Fold folda.1 — Globin-like
Superfamily Superfamily superfamilya.1.1 — Globin-like
Family Family familya.1.1.2 — Globins
Domain ID domain_idd3wyob_
Class classa — All alpha proteins
Fold Fold folda.1 — Globin-like
Superfamily Superfamily superfamilya.1.1 — Globin-like
Family Family familya.1.1.2 — Globins
Domain ID domain_idd3wyoc_
Class classa — All alpha proteins
Fold Fold folda.1 — Globin-like
Superfamily Superfamily superfamilya.1.1 — Globin-like
Family Family familya.1.1.2 — Globins
Domain ID domain_idd3wyod_
Class classa — All alpha proteins
Fold Fold folda.1 — Globin-like
Superfamily Superfamily superfamilya.1.1 — Globin-like
Family Family familya.1.1.2 — Globins

CATH v4.4 (8 domains)

Domain ID domain_id3wyoA01
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily2100
Domain ID domain_id3wyoA02
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily2110
Domain ID domain_id3wyoB01
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily2100
Domain ID domain_id3wyoB02
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily2110
Domain ID domain_id3wyoC01
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily2100
Domain ID domain_id3wyoC02
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily2110
Domain ID domain_id3wyoD01
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily2100
Domain ID domain_id3wyoD02
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily2110

8. Citations (1)

9. Files and Curves (10)