SAXSdb — 3mba

▼

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

MYOGLOBIN

Aplysia limacina

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 1–145	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 experimental conditions	Resolution 2.00 Å

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 3MBA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DM1 2.0 A CRYSTAL STRUCTURE OF THE DOUBLE MUTANT H(E7)V, T(E10)R OF MYOGLOBIN FROM APLYSIA LIMACINA Deposited 1999-12-13	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 1–146（146 aa）	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
1MBA APLYSIA LIMACINA MYOGLOBIN. CRYSTALLOGRAPHIC ANALYSIS AT 1.6 ANGSTROMS RESOLUTION Deposited 1989-02-22	Different ligand/ion 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 ligand/ion 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 construct Different ligand/ion	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
4MBA APLYSIA LIMACINA MYOGLOBIN. CRYSTALLOGRAPHIC ANALYSIS AT 1.6 ANGSTROMS RESOLUTION Deposited 1989-02-22	Different ligand/ion	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 ligand/ion 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 2–146； UniProt 1–145

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3mba
Deposition date deposition_date	1989-02-22
Structure title title	APLYSIA LIMACINA MYOGLOBIN. CRYSTALLOGRAPHIC ANALYSIS AT 1.6 ANGSTROMS RESOLUTION
Keywords keywords	OXYGEN STORAGE; OXYGEN STORAGE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	15.68 Å
Radius of gyration Rg (electron density) rg_electron	14.24 Å
Forward intensity I(0) i0	4656190.00
Molecular weight molecular_weight	15988.0 kDa
Excluded volume excluded_volume	20212 Å³
Envelope volume envelope_volume	21615 Å³
Hydration-shell volume shell_volume	12907 Å³
Envelope diameter envelope_diameter	47.4 Å
Shell Rg shell_rg	20.06 Å
Envelope Rg envelope_rg	14.43 Å
Shape Rg shape_rg	14.19 Å
Total Rg total_rg	15.56 Å
Total atoms total_atoms	1130
Residues n_residues	146
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

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

Maximum dimension Dmax dmax	49.0 Å
Rg (real space) rg_real	15.57 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	4.6560e+06
I(0) uncertainty (real space) i0_real_error	5.6910e+04
Rg (reciprocal space) rg_reciprocal	15.58 Å
I(0) (reciprocal space) i0_reciprocal	4656000.0000
Solution quality estimate total_estimate	0.8906
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.1 Å
Skewness Skewness skewness	0.080
Kurtosis Kurtosis kurtosis	-0.356
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	708300.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.862; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.999

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	MYOGLOBIN
Molecular weight formula_weight	15349.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1331

XSLSAAEADLAGKSWAPVFANKNANGLDFLVALFEKFPDSANFFADFKGKSVADIKASPKLRDVSSRIFTRLNEFVNNAANAGKMSAMLSQFAKEHVGFGVGSAQFENVRSMFPGFVASVAAPPAGADAAWTKLFGLIIDALKAAGA

来源 Source

来源生物 organism	Aplysia limacina
通用名 common_name	slug sea hare
NCBI Class编号 ncbi_taxonomy_id	6502

Entity 2 Entity 2 non-polymer

Description description	FLUORIDE ION
Molecular weight formula_weight	19.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	201

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3mbaa_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.2 — Globins

CATH v4.4 (1 domains)

Domain ID domain_id	3mbaA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

▶

8. Citations (8)

Aplysia limacina myoglobin. Crystallographic analysis at 1.6 A resolution.

J.Mol.Biol. (1989)

PMID: 2926816 · DOI: 10.1016/0022-2836(89)90224-6 PRIMARY

Crystal Structure of Ferric Aplysia Limacina Myoglobin at 2.0 Angstroms Resolution

J.Mol.Biol. (1985)

Reactivity of Ferric Aplysia and Sperm Whale Myoglobins Towards Imidazole. X-Ray and Binding Study

J.Mol.Biol. (1982)

The Structure of Aplysia Limacina Myoglobin at 3.6 Angstroms Resolution

Acta Crystallogr.,Sect.A (Supplement) (1978)

The Crystal Structure of met-Myoglobin from Aplysia Limacina at 5 Angstroms Resolution

Acta Crystallogr.,Sect.B (1978)

Crystallization and Preliminary X-Ray Diffraction Studies on met-Myoglobin from Aplysia Limacina

J.Mol.Biol. (1975)

The Amino Acid Sequence of Myoglobin from the Mollusc Aplysia Limacina

Int.J.Pept.Protein Res. (1973)

Aplysia Limacina Myoglobin. Molecular Bases for Ligand Binding and Reversible Unfolding

To be Published

▶

Unit-cell length a length_a	52.980 Å
Unit-cell length b length_b	70.700 Å
Unit-cell length c length_c	32.500 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	0.1420
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/mb/3mba/3mba.fit
pddf	/app/data/pr_computation/mb/3mba/3mba.pr.out
profile	/app/data/saxs_computation/mb/3mba/3mba.dat

APLYSIA LIMACINA MYOGLOBIN. CRYSTALLOGRAPHIC ANALYSIS AT 1.6 ANGSTROMS RESOLUTION