1do7

CARBONMONOXY-MYOGLOBIN (MUTANT L29W) REBINDING STRUCTURE AFTER PHOTOLYSIS AT T< 180K

Method: X-RAY DIFFRACTION Dmax: 53.0 Å Quality: GOOD

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

MYOGLOBIN

Physeter catodon

UniProt P02185

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 1–153 Mutation:M0(FME), L29W, D122N Non-standard monomer:Yes (specific site not provided by mmCIF) alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose × 1 SO4 SULFATE ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CMO CARBON MONOXIDE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:BATCH CRYSTALLIZATION;pH 8.5;292 K;CRYSTALS WERE GROWN IN 2.5M AMMONIUM SULFATE SOLUTION, BUFFERED WITH 20MM TRIS/ HCL TO PH 8.5. THE CRYSTALLIZATION SOLUTION WAS REPLACED IN STEPS AGAINST A SOLUTION CONTAINING 2.5M AMMONIUM SULFATE, 20MM TRIS, 300MG/ML TREHALOSE AT PH 8.5., BATCH CRYSTALLIZATION, temperature 292K Resolution 1.85 Å R-free 0.214

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.

354 other PDB entries and 366 assemblies. Open the comparison page and filter oligomeric states

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

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 1do7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1do7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1do7
Deposition date deposition_date1999-12-19
Structure title titleCARBONMONOXY-MYOGLOBIN (MUTANT L29W) REBINDING STRUCTURE AFTER PHOTOLYSIS AT T< 180K
Keywords keywordsHEME, RESPIRATORY PROTEIN, PHOTOLYSED MYOGLOBIN, LIGAND MIGRATION, OXYGEN STORAGE-TRANSPORT COMPLEX; OXYGEN STORAGE/TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier16.67
Radius of gyration Rg (electron density) rg_electron15.16
Forward intensity I(0) i06192420.00
Molecular weight molecular_weight18455.0 kDa
Excluded volume excluded_volume23276 ų
Envelope volume envelope_volume25761 ų
Hydration-shell volume shell_volume14302 ų
Envelope diameter envelope_diameter53.9
Shell Rg shell_rg21.09
Envelope Rg envelope_rg15.41
Shape Rg shape_rg15.10
Total Rg total_rg16.43
Total atoms total_atoms1301
Residues n_residues153
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 dmax53.0
Rg (real space) rg_real16.56
Rg uncertainty (real space) rg_real_error0.33
I(0) (real space) i0_real6.1920e+06
I(0) uncertainty (real space) i0_real_error7.2970e+04
Rg (reciprocal space) rg_reciprocal16.57
I(0) (reciprocal space) i0_reciprocal6192000.0000
Solution quality estimate total_estimate0.8141
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary21.3
Skewness Skewness skewness0.098
Kurtosis Kurtosis kurtosis-0.423
Angular range angular_range— – 0.4750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha962800.0000
Real-space data points n_real_points78
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.865; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1do7a_
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 (1 domains)

Domain ID domain_id1do7A00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins

8. Citations (1)

9. Files and Curves (10)