SAXSdb — 1a7e

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

MYOHEMERYTHRIN

Themiste zostericola

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 1–118	Mutation：L103N	CL CHLORIDE ION × 2 OFO HYDROXY DIIRON-OXO MOIETY × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；27% PEG 6K, 100MM HEPES, 1.0M LICL (PH 7.0)	Resolution 1.80 Å R-free 0.227

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 1A7E	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A7D CHLOROMET MYOHEMERYTHRIN FROM THEMISTE ZOSTERICOLA Deposited 1998-03-12	Different mutation/modification Different ligand/ion	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–118（118 aa）	Not recorded	CL CHLORIDE ION × 2 CFO CHLORO DIIRON-OXO MOIETY × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；27% PEG 6K, 100MM HEPES, 1.0M LICL (PH 7.0)	Resolution 1.80 Å R-free 0.227
2IGF CRYSTAL STRUCTURES OF AN ANTIBODY TO A PEPTIDE AND ITS COMPLEX WITH PEPTIDE ANTIGEN AT 2.8 ANGSTROMS Deposited 1991-03-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain P 69–87（19 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
2IGF CRYSTAL STRUCTURES OF AN ANTIBODY TO A PEPTIDE AND ITS COMPLEX WITH PEPTIDE ANTIGEN AT 2.8 ANGSTROMS Deposited 1991-03-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain P 69–87（19 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
2MHR STRUCTURE OF MYOHEMERYTHRIN IN THE AZIDOMET STATE AT 1.7(SLASH)1.3 ANGSTROMS RESOLUTION Deposited 1987-04-20	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–118（118 aa）	Not recorded	AZI AZIDE ION × 1 SO4 SULFATE ION × 3 FEO MU-OXO-DIIRON × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.30 Å

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HEMTM_THEZO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–118； UniProt 1–118

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	1a7e
Deposition date deposition_date	1998-03-12
Structure title title	HYDROXOMET MYOHEMERYTHRIN FROM THEMISTE ZOSTERICOLA
Keywords keywords	NONHEME IRON OXYGEN CARRIER, 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	14.82 Å
Radius of gyration Rg (electron density) rg_electron	13.72 Å
Forward intensity I(0) i0	3900030.00
Molecular weight molecular_weight	13991.0 kDa
Excluded volume excluded_volume	17452 Å³
Envelope volume envelope_volume	18965 Å³
Hydration-shell volume shell_volume	11798 Å³
Envelope diameter envelope_diameter	49.9 Å
Shell Rg shell_rg	19.44 Å
Envelope Rg envelope_rg	14.11 Å
Shape Rg shape_rg	13.68 Å
Total Rg total_rg	15.00 Å
Total atoms total_atoms	1188
Residues n_residues	118
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	50.4 Å
Rg (real space) rg_real	14.76 Å
Rg uncertainty (real space) rg_real_error	0.33 Å
I(0) (real space) i0_real	3.9000e+06
I(0) uncertainty (real space) i0_real_error	4.8320e+04
Rg (reciprocal space) rg_reciprocal	14.77 Å
I(0) (reciprocal space) i0_reciprocal	3900000.0000
Solution quality estimate total_estimate	0.8640
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.2 Å
Skewness Skewness skewness	0.269
Kurtosis Kurtosis kurtosis	-0.233
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	988700.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.752; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.981

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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	MYOHEMERYTHRIN
Molecular weight formula_weight	13801.7 kDa
Mutation mutation	L103N
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	1800

GWEIPEPYVWDESFRVFYEQLDEEHKKIFKGIFDCIRDNSAPNLATLVKVTTNHFTHEEAMMDAAKYSEVVPHKKMHKDFLEKIGGLSAPVDAKNVDYCKEWNVNHIKGTDFKYKGKL

来源 Source

来源生物 organism	Themiste zostericola
NCBI Class编号 ncbi_taxonomy_id	6437
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	HYDROXY DIIRON-OXO MOIETY
Molecular weight formula_weight	144.7 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	204

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1a7ea_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.4 — Hemerythrin-like
Family Family family	a.24.4.1 — Hemerythrin-like

CATH v4.4 (1 domains)

Domain ID domain_id	1a7eA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	50 — Hemerythrin-like

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8. Citations (1)

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Unit-cell length a length_a	41.885 Å
Unit-cell length b length_b	81.170 Å
Unit-cell length c length_c	36.685 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1860
R_work r_work	0.1860
R_free r_free	0.2270

fit	/app/data/saxs_computation/a7/1a7e/1a7e.fit
pddf	/app/data/pr_computation/a7/1a7e/1a7e.pr.out
profile	/app/data/saxs_computation/a7/1a7e/1a7e.dat

HYDROXOMET MYOHEMERYTHRIN FROM THEMISTE ZOSTERICOLA

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

MYOHEMERYTHRIN

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