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9r3p

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

Method: X-RAY DIFFRACTION D_max: 83.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

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

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	25.24 Å
rg_electron	24.35 Å
i0	20066800.00
molecular_weight	35381.0 kDa
excluded_volume	44736 Å³
envelope_volume	53318 Å³
shell_volume	19314 Å³
envelope_diameter	88.6 Å
shell_rg	29.92 Å
envelope_rg	24.39 Å
shape_rg	24.34 Å
total_rg	25.09 Å
total_atoms	2493
n_residues	302
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	83.8 Å
rg_real	25.39 Å
rg_real_error	0.47 Å
i0_real	2.0070e+07
i0_real_error	2.7960e+05
rg_reciprocal	25.34 Å
i0_reciprocal	20070000.0000
total_estimate	0.8636
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.9 Å
skewness	0.425
kurtosis	-0.537
angular_range	— – 0.3150 Å⁻¹
current_alpha	0.0001
highest_alpha	3094000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.838; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.714; Smooth: 0.996

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Atypical leghemoglobin 2-1
formula_weight	18283.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	2664

ASWSHPQFEKGATFSEEQEALVNSSWEAFSQNIPQLSIIFYTSILEKAPEAKAMFSFLKDSDGVPKDNLDLEAHCEKVFELTRNSALQLRAKGKVEVERIALKFLGYVHAQRRVLDPHFLVLKEALLKTLKEAMGDKWSEEVSNAWGIAYDELAGVIKKGMS

Source

organism	Lotus japonicus
ncbi_taxonomy_id	34305
host_organism	Escherichia coli

Entity 2 non-polymer

description	PROTOPORPHYRIN IX CONTAINING FE
formula_weight	616.5 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	CYANIDE ION
formula_weight	26.0 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	171

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6. Citations (1)

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length_a	35.928 Å
length_b	127.656 Å
length_c	152.733 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	C 2 2 21
int_tables_number	20
crystal_system	—

resolution	1.600 Å
resolution_low	76.370 Å
r_factor	0.1798
r_work	0.1784
r_free	0.2056

fit	/app/data/saxs_computation/r3/9r3p/9r3p.fit
pddf	/app/data/pr_computation/r3/9r3p/9r3p.pr.out
profile	/app/data/saxs_computation/r3/9r3p/9r3p.dat