SAXSdb — 1d8u

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

NON-SYMBIOTIC HEMOGLOBIN

Oryza sativa

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–166 Chain B； UniProt 1–166	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；295 K；AMMONIUM PHOSPHATE, SUCROSE, POTASSIUM PHOSPHATE, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 22K	Resolution 2.35 Å R-free 0.261

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 1D8U	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2GNV Crystal structure of non-symbiotic plant hemoglobin from rice, B10 mutant F40L Deposited 2006-04-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–166（165 aa） Chain B 2–166（165 aa）	Mutation：F40L Mutation：F40L	HEM PROTOPORPHYRIN IX CONTAINING FE × 2 DIO 1,4-DIETHYLENE DIOXIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；1.9M Ammonium Phosphate, 10mM Potassium Phosphate, 20% Sucrose, 3% Dioxane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.30 Å R-free 0.247
2GNW Crystal structure of non-symbiotic plant hemoglobin from rice, B10 mutant F40W Deposited 2006-04-11	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–166（165 aa） Chain B 2–166（165 aa）	Mutation：F40W Mutation：F40W	HEM PROTOPORPHYRIN IX CONTAINING FE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；1.9M Ammonium Phosphate, 10mM Potassium Phosphate, 20% Sucrose, 3% Dioxane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.204

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

View Construct and Data Evidence

UniProt name	HBL1_ORYSA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–166； UniProt 1–166 Author chain B； PDBConstruct 1–166； UniProt 1–166

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	1d8u
Deposition date deposition_date	1999-10-26
Structure title title	CRYSTAL STRUCTURE OF NON-SYMBIOTIC PLANT HEMOGLOBIN FROM RICE
Keywords keywords	GLOBIN, BIS-HISTIDYL, HEME PROTEIN, OXYGEN STORAGE/TRANSPORT, OXYGEN STORAGE-TRANSPORT complex; OXYGEN STORAGE/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	22.65 Å
Radius of gyration Rg (electron density) rg_electron	21.41 Å
Forward intensity I(0) i0	22798900.00
Molecular weight molecular_weight	37860.0 kDa
Excluded volume excluded_volume	48056 Å³
Envelope volume envelope_volume	58654 Å³
Hydration-shell volume shell_volume	22774 Å³
Envelope diameter envelope_diameter	71.1 Å
Shell Rg shell_rg	28.04 Å
Envelope Rg envelope_rg	21.59 Å
Shape Rg shape_rg	21.35 Å
Total Rg total_rg	22.50 Å
Total atoms total_atoms	2662
Residues n_residues	330
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	70.2 Å
Rg (real space) rg_real	22.56 Å
Rg uncertainty (real space) rg_real_error	0.38 Å
I(0) (real space) i0_real	2.2800e+07
I(0) uncertainty (real space) i0_real_error	2.7880e+05
Rg (reciprocal space) rg_reciprocal	22.59 Å
I(0) (reciprocal space) i0_reciprocal	22800000.0000
Solution quality estimate total_estimate	0.9116
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.7 Å
Skewness Skewness skewness	0.183
Kurtosis Kurtosis kurtosis	-0.490
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3712000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.951; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.996

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	NON-SYMBIOTIC HEMOGLOBIN
Molecular weight formula_weight	18469.4 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	2865

MALVEDNNAVAVSFSEEQEALVLKSWAILKKDSANIALRFFLKIFEVAPSASQMFSFLRNSDVPLEKNPKLKTHAMSVFVMTCEAAAQLRKAGKVTVRDTTLKRLGATHLKYGVGDAHFEVVKFALLDTIKEEVPADMWSPAMKSAWSEAYDHLVAAIKQEMKPAE

来源 Source

来源生物 organism	Oryza sativa
通用名 common_name	rice
NCBI Class编号 ncbi_taxonomy_id	4530
宿主生物 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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	203

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1d8ua_
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	d1d8ub_
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	1d8uA00
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	1d8uB00
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	126.800 Å
Unit-cell length b length_b	126.800 Å
Unit-cell length c length_c	55.500 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.2080
R_free r_free	0.2610

fit	/app/data/saxs_computation/d8/1d8u/1d8u.fit
pddf	/app/data/pr_computation/d8/1d8u/1d8u.pr.out
profile	/app/data/saxs_computation/d8/1d8u/1d8u.dat

CRYSTAL STRUCTURE OF NON-SYMBIOTIC PLANT HEMOGLOBIN FROM RICE

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

NON-SYMBIOTIC HEMOGLOBIN

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