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1dm1

2.0 A CRYSTAL STRUCTURE OF THE DOUBLE MUTANT H(E7)V, T(E10)R OF MYOGLOBIN FROM APLYSIA LIMACINA

Method: X-RAY DIFFRACTION Dmax: 49.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

MYOGLOBIN

Aplysia limacina

UniProt P02210

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–146 Mutation：V63H, R66T HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；SODIUM CITRATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.99 Å R-free 0.216

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.

Other PDB Difference from Current Entry 1DM1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1MBA APLYSIA LIMACINA MYOGLOBIN. CRYSTALLOGRAPHIC ANALYSIS AT 1.6 ANGSTROMS RESOLUTION Deposited 1989-02-22 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–145（145 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.60 Å
2FAL X-RAY CRYSTAL STRUCTURE OF FERRIC APLYSIA LIMACINA MYOGLOBIN IN DIFFERENT LIGANDED STATES Deposited 1993-06-14 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–145（145 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CYN CYANIDE ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.80 Å
2FAM X-RAY CRYSTAL STRUCTURE OF FERRIC APLYSIA LIMACINA MYOGLOBIN IN DIFFERENT LIGANDED STATES Deposited 1993-07-20 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–146（146 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SCN THIOCYANATE ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
3MBA APLYSIA LIMACINA MYOGLOBIN. CRYSTALLOGRAPHIC ANALYSIS AT 1.6 ANGSTROMS RESOLUTION Deposited 1989-02-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–145（145 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) F FLUORIDE ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
4MBA APLYSIA LIMACINA MYOGLOBIN. CRYSTALLOGRAPHIC ANALYSIS AT 1.6 ANGSTROMS RESOLUTION Deposited 1989-02-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–145（145 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) HEM PROTOPORPHYRIN IX CONTAINING FE × 1 IMD IMIDAZOLE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
5MBA BINDING MODE OF AZIDE TO FERRIC APLYSIA LIMACINA MYOGLOBIN. CRYSTALLOGRAPHIC ANALYSIS AT 1.9 ANGSTROMS RESOLUTION Deposited 1991-01-14 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–145（145 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) AZI AZIDE ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.90 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GLB_APLLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–146； UniProt 1–146

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 1dm1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1dm1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1dm1
Deposition date deposition_date1999-12-13
Structure title title2.0 A CRYSTAL STRUCTURE OF THE DOUBLE MUTANT H(E7)V, T(E10)R OF MYOGLOBIN FROM APLYSIA LIMACINA
Keywords keywordsGLOBIN FOLD, OXYGEN STORAGE-TRANSPORT COMPLEX; OXYGEN STORAGE/TRANSPORT
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier15.65 Å
Radius of gyration Rg (electron density) rg_electron14.24 Å
Forward intensity I(0) i04621030.00
Molecular weight molecular_weight15865.0 kDa
Excluded volume excluded_volume20004 ų
Envelope volume envelope_volume21395 ų
Hydration-shell volume shell_volume12826 ų
Envelope diameter envelope_diameter47.8 Å
Shell Rg shell_rg20.01 Å
Envelope Rg envelope_rg14.38 Å
Shape Rg shape_rg14.18 Å
Total Rg total_rg15.53 Å
Total atoms total_atoms1122
Residues n_residues146
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax49.8 Å
Rg (real space) rg_real15.54 Å
Rg uncertainty (real space) rg_real_error0.30 Å
I(0) (real space) i0_real4.6210e+06
I(0) uncertainty (real space) i0_real_error4.6190e+04
Rg (reciprocal space) rg_reciprocal15.55 Å
I(0) (reciprocal space) i0_reciprocal4621000.0000
Solution quality estimate total_estimate0.8808
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.4 Å
Skewness Skewness skewness0.069
Kurtosis Kurtosis kurtosis-0.367
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha711300.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.828; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.969
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1dm1a_
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_id1dm1A00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
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8. Citations (1)

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9. Files and Curves (10)