6ltm

The dimeric structure of G80A/H81A/H82A myoglobin

Method: X-RAY DIFFRACTION Dmax: 81.9 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:G80A/H81A/H82A HEM PROTOPORPHYRIN IX CONTAINING FE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;277 K;0.1M Tris-HCl buffer, 0.1M sodium acetate, 12.5% (w/v) PEG 6000 Resolution 1.65 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.

149 other PDB entries and 156 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MYG_HORSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–153; UniProt 2–154 Author chain B; 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 6ltm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6ltm
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id6ltm
Deposition date deposition_date2020-01-22
Structure title titleThe dimeric structure of G80A/H81A/H82A myoglobin
Keywords keywordsOXYGEN STORAGE, 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_guinier24.06
Radius of gyration Rg (electron density) rg_electron23.34
Forward intensity I(0) i019398200.00
Molecular weight molecular_weight34900.0 kDa
Excluded volume excluded_volume44308 ų
Envelope volume envelope_volume51942 ų
Hydration-shell volume shell_volume19872 ų
Envelope diameter envelope_diameter85.6
Shell Rg shell_rg28.63
Envelope Rg envelope_rg23.42
Shape Rg shape_rg23.33
Total Rg total_rg24.08
Total atoms total_atoms2466
Residues n_residues306
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 dmax81.9
Rg (real space) rg_real24.23
Rg uncertainty (real space) rg_real_error0.76
I(0) (real space) i0_real1.9400e+07
I(0) uncertainty (real space) i0_real_error2.8850e+05
Rg (reciprocal space) rg_reciprocal24.19
I(0) (reciprocal space) i0_reciprocal19400000.0000
Solution quality estimate total_estimate0.7777
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.0
Skewness Skewness skewness0.496
Kurtosis Kurtosis kurtosis-0.296
Angular range angular_range— – 0.3300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4369000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.764; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.814; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6ltma_
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_idd6ltmb_
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 (4 domains)

Domain ID domain_id6ltmA01
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily2100
Domain ID domain_id6ltmA02
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily2110
Domain ID domain_id6ltmB01
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily2100
Domain ID domain_id6ltmB02
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily2110

8. Citations (1)

9. Files and Curves (10)