SAXSdb — 9r3p

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

Atypical leghemoglobin 2-1

Lotus japonicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	PROTOPORPHYRIN IX CONTAINING FE × 1 CYANIDE ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	PROTOPORPHYRIN IX CONTAINING FE × 1 CYANIDE ION × 1 PHOSPHATE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GLB21_LOTJA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 12–162； UniProt 2–152 Author chain B； PDBConstruct 12–162； UniProt 2–152

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	9r3p
Deposition date deposition_date	2025-05-05
Last revision last_revision	2026-05-13
Structure title title	Hemoglobin Glb2-1 of Lotus japonicus (cyano-ferric form)
Keywords keywords	HEME, MULTIGENE FAMILY, OXYGEN BINDING, HEXACOORDINATION (FERRIC FORM), TYROSINE (B10); OXYGEN BINDING
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9r3p__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9r3p__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9r3p__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	16.54 Å
Rg (electron density)	15.02 Å
Total Rg	16.28 Å
Atom count	1244
Residues	151
Excluded volume	22347 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9r3p__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9r3p__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Atypical leghemoglobin 2-1
Molecular weight formula_weight	18283.8 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	2664

ASWSHPQFEKGATFSEEQEALVNSSWEAFSQNIPQLSIIFYTSILEKAPEAKAMFSFLKDSDGVPKDNLDLEAHCEKVFELTRNSALQLRAKGKVEVERIALKFLGYVHAQRRVLDPHFLVLKEALLKTLKEAMGDKWSEEVSNAWGIAYDELAGVIKKGMS

Source Source

Source organism organism	Lotus japonicus
NCBI taxonomy ID ncbi_taxonomy_id	34305
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 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 3 Entity 3 non-polymer

Description description	CYANIDE ION
Molecular weight formula_weight	26.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	171

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Unit-cell length a length_a	35.928 Å
Unit-cell length b length_b	127.656 Å
Unit-cell length c length_c	152.733 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	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	76.370 Å
R factor r_factor	0.1798
R_work r_work	0.1784
R_free r_free	0.2056

Hemoglobin Glb2-1 of Lotus japonicus (cyano-ferric form)

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

Atypical leghemoglobin 2-1

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9r3p__assembly_1__model_1

9r3p__assembly_1__model_1 | I(q)

9r3p__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)

Hemoglobin Glb2-1 of Lotus japonicus (cyano-ferric form)

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

Atypical leghemoglobin 2-1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9r3p__assembly_1__model_1

9r3p__assembly_1__model_1 | I(q)

9r3p__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)