SAXSdb — 1uvy

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

MYOGLOBIN

PARAMECIUM CAUDATUM

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 1–116	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 XE XENON × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；AMMONIUM SULPHATE, SODIUM ACETATE, pH 6.00	Resolution 2.40 Å R-free 0.282

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 1UVY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DLW X-RAY CRYSTAL STRUCTURE OF TRUNCATED HEMOGLOBIN FROM P.CAUDATUM. Deposited 1999-12-13	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–116（116 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；AMMONIUM SULPHATE, SODIUM ACETATE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.54 Å R-free 0.183

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

View Construct and Data Evidence

UniProt name	GLB_PARCA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–116； UniProt 1–116

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	1uvy
Deposition date deposition_date	2004-01-27
Structure title title	HEME-LIGAND TUNNELING IN GROUP I TRUNCATED HEMOGLOBINS
Keywords keywords	OXYGEN STORAGE/TRANSPORT, LIGAND DIFFUSION, HEME, 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	14.32 Å
Radius of gyration Rg (electron density) rg_electron	12.95 Å
Forward intensity I(0) i0	3334210.00
Molecular weight molecular_weight	12636.0 kDa
Excluded volume excluded_volume	15654 Å³
Envelope volume envelope_volume	16729 Å³
Hydration-shell volume shell_volume	11034 Å³
Envelope diameter envelope_diameter	42.8 Å
Shell Rg shell_rg	18.68 Å
Envelope Rg envelope_rg	13.22 Å
Shape Rg shape_rg	12.96 Å
Total Rg total_rg	14.12 Å
Total atoms total_atoms	881
Residues n_residues	116
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	44.8 Å
Rg (real space) rg_real	14.22 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	3.3340e+06
I(0) uncertainty (real space) i0_real_error	3.2280e+04
Rg (reciprocal space) rg_reciprocal	14.23 Å
I(0) (reciprocal space) i0_reciprocal	3334000.0000
Solution quality estimate total_estimate	0.8796
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.8 Å
Skewness Skewness skewness	0.087
Kurtosis Kurtosis kurtosis	-0.366
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	594600.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.850; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.895

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	MYOGLOBIN
Molecular weight formula_weight	11914.3 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	918

SLFEQLGGQAAVQAVTAQFYANIQADATVATFFNGIDMPNQTNKTAAFLCAALGGPNAWTGRNLKEVHANMGVSNAQFTTVIGHLRSALTGAGVAAALVEQTVAVAETVRGDVVTV

来源 Source

来源生物 organism	PARAMECIUM CAUDATUM
NCBI Class编号 ncbi_taxonomy_id	5885
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	1

Entity 3 Entity 3 non-polymer

Description description	XENON
Molecular weight formula_weight	131.3 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	37

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1uvya_
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.1.1.1 — Truncated hemoglobin

CATH v4.4 (1 domains)

Domain ID domain_id	1uvyA00
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	61.380 Å
Unit-cell length b length_b	61.380 Å
Unit-cell length c length_c	33.840 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 43
Space-group number int_tables_number	78
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2110
R_work r_work	0.2110
R_free r_free	0.2820

fit	/app/data/saxs_computation/uv/1uvy/1uvy.fit
pddf	/app/data/pr_computation/uv/1uvy/1uvy.pr.out
profile	/app/data/saxs_computation/uv/1uvy/1uvy.dat

HEME-LIGAND TUNNELING IN GROUP I TRUNCATED HEMOGLOBINS

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

MYOGLOBIN

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