SAXSdb — 1bin

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

LEGHEMOGLOBIN A

Glycine max

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 1–143	Not recorded	ACT ACETATE ION × 1 SO4 SULFATE ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.8；pH 6.8	Resolution 2.20 Å R-free 0.297
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–143	Not recorded	ACT ACETATE ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.8；pH 6.8	Resolution 2.20 Å R-free 0.297

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 1BIN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1FSL FERRIC SOYBEAN LEGHEMOGLOBIN COMPLEXED WITH NICOTINATE Deposited 1995-12-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–143（143 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NIO NICOTINIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0	Resolution 2.30 Å
1FSL FERRIC SOYBEAN LEGHEMOGLOBIN COMPLEXED WITH NICOTINATE Deposited 1995-12-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–143（143 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NIO NICOTINIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0	Resolution 2.30 Å

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LGBA_SOYBN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–143； UniProt 1–143 Author chain B； PDBConstruct 1–143； UniProt 1–143

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1bin
Deposition date deposition_date	1996-08-23
Structure title title	LEGHEMOGLOBIN A (ACETOMET)
Keywords keywords	HEME, NITROGEN FIXATION, MULTIGENE FAMILY, OXYGEN TRANSPORT; OXYGEN TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	20.31 Å
Radius of gyration Rg (electron density) rg_electron	19.07 Å
Forward intensity I(0) i0	16071800.00
Molecular weight molecular_weight	31930.0 kDa
Excluded volume excluded_volume	40626 Å³
Envelope volume envelope_volume	46040 Å³
Hydration-shell volume shell_volume	20058 Å³
Envelope diameter envelope_diameter	60.7 Å
Shell Rg shell_rg	25.33 Å
Envelope Rg envelope_rg	19.13 Å
Shape Rg shape_rg	19.04 Å
Total Rg total_rg	20.06 Å
Total atoms total_atoms	2257
Residues n_residues	286
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

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

Maximum dimension Dmax dmax	59.5 Å
Rg (real space) rg_real	20.18 Å
Rg uncertainty (real space) rg_real_error	0.33 Å
I(0) (real space) i0_real	1.6070e+07
I(0) uncertainty (real space) i0_real_error	1.8690e+05
Rg (reciprocal space) rg_reciprocal	20.21 Å
I(0) (reciprocal space) i0_reciprocal	16070000.0000
Solution quality estimate total_estimate	0.9099
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.3 Å
Skewness Skewness skewness	0.075
Kurtosis Kurtosis kurtosis	-0.569
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3464000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.957; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.963

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	LEGHEMOGLOBIN A
Molecular weight formula_weight	15260.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2392

VAFTEKQDALVSSSFEAFKANIPQYSVVFYTSILEKAPAAKDLFSFLANGVDPTNPKLTGHAEKLFALVRDSAGQLKASGTVVADAALGSVHAQKAVTDPQFVVVKEALLKTIKAAVGDKWSDELSRAWEVAYDELAAAIKKA

来源 Source

来源生物 organism	Glycine max
通用名 common_name	soybean
NCBI Class编号 ncbi_taxonomy_id	3847
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	135

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1bina_
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

Domain ID domain_id	d1binb_
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 (2 domains)

Domain ID domain_id	1binA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

Domain ID domain_id	1binB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

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8. Citations (1)

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Unit-cell length a length_a	34.980 Å
Unit-cell length b length_b	53.390 Å
Unit-cell length c length_c	141.730 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	8

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

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1980
R_work r_work	0.1980
R_free r_free	0.2970

fit	/app/data/saxs_computation/bi/1bin/1bin.fit
pddf	/app/data/pr_computation/bi/1bin/1bin.pr.out
profile	/app/data/saxs_computation/bi/1bin/1bin.dat

LEGHEMOGLOBIN A (ACETOMET)

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

LEGHEMOGLOBIN A

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction