SAXSdb — 1a7w

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

HISTONE HMFB

Methanothermus fervidus

UniProt P19267

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 1–69	Not recorded	ZN ZINC ION × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.55 Å R-free 0.248

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 1A7W	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B6W CRYSTAL STRUCTURE OF THE SELENOMETHIONINE VARIANT OF HISTONE HMFB FROM METHANOTHERMUS FERVIDUS Deposited 1999-01-19	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 1–69（69 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.05 Å R-free 0.260
1BFM HISTONE B FROM METHANOTHERMUS FERVIDUS Deposited 1995-09-28	Different construct Different mutation/modification Different ligand/ion Different experimental method Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–69（69 aa） Chain B 1–69（69 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
5T5K Structure of histone-based chromatin in Archaea Deposited 2016-08-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 6 PDB declaration: octameric	Chain A 1–69（69 aa） Chain B 1–69（69 aa） Chain C 1–69（69 aa） Chain D 1–69（69 aa） Chain E 1–69（69 aa） Chain F 1–69（69 aa）	Not recorded	CAC CACODYLATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；100 mM MgAc, 50 mM Na Cacodylate pH 6.5, 10% PEG 400 under silicon oil	Resolution 4.00 Å R-free 0.262

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

View Construct and Data Evidence

UniProt name	HMFB_METFE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–69； UniProt 1–69

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	1a7w
Deposition date deposition_date	1998-03-18
Structure title title	CRYSTAL STRUCTURE OF THE HISTONE HMFB FROM METHANOTHERMUS FERVIDUS
Keywords keywords	HISTONE; HISTONE
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	16.57 Å
Radius of gyration Rg (electron density) rg_electron	15.59 Å
Forward intensity I(0) i0	1252200.00
Molecular weight molecular_weight	7625.0 kDa
Excluded volume excluded_volume	9554 Å³
Envelope volume envelope_volume	12270 Å³
Hydration-shell volume shell_volume	7368 Å³
Envelope diameter envelope_diameter	56.9 Å
Shell Rg shell_rg	19.70 Å
Envelope Rg envelope_rg	15.77 Å
Shape Rg shape_rg	15.63 Å
Total Rg total_rg	16.40 Å
Total atoms total_atoms	529
Residues n_residues	68
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	57.9 Å
Rg (real space) rg_real	16.75 Å
Rg uncertainty (real space) rg_real_error	0.54 Å
I(0) (real space) i0_real	1.2520e+06
I(0) uncertainty (real space) i0_real_error	1.6570e+04
Rg (reciprocal space) rg_reciprocal	16.73 Å
I(0) (reciprocal space) i0_reciprocal	1252000.0000
Solution quality estimate total_estimate	0.7477
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	4
Primary peak position r_peak_primary	13.5 Å
Skewness Skewness skewness	0.400
Kurtosis Kurtosis kurtosis	-0.478
Angular range angular_range	— – 0.4800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	130200.0000
Real-space data points n_real_points	78
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.739; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.499; Smooth: 0.000

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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	HISTONE HMFB
Molecular weight formula_weight	7683.1 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	581

MELPIAPIGRIIKDAGAERVSDDARITLAKILEEMGRDIASEAIKLARHAGRKTIKAEDIELAVRRFKK

来源 Source

来源生物 organism	Methanothermus fervidus
NCBI Class编号 ncbi_taxonomy_id	2180
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 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	46

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1a7wa_
Class class	a — All alpha proteins
Fold Fold fold	a.22 — Histone-fold
Superfamily Superfamily superfamily	a.22.1 — Histone-fold
Family Family family	a.22.1.2 — Archaeal histone

CATH v4.4 (1 domains)

Domain ID domain_id	1a7wA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

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8. Citations (3)

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Unit-cell length a length_a	31.300 Å
Unit-cell length b length_b	61.580 Å
Unit-cell length c length_c	39.650 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.550 Å
Low-resolution limit resolution_low	18.000 Å
R factor r_factor	0.2000
R_work r_work	0.1980
R_free r_free	0.2480

fit	/app/data/saxs_computation/a7/1a7w/1a7w.fit
pddf	/app/data/pr_computation/a7/1a7w/1a7w.pr.out
profile	/app/data/saxs_computation/a7/1a7w/1a7w.dat

CRYSTAL STRUCTURE OF THE HISTONE HMFB FROM METHANOTHERMUS FERVIDUS

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

HISTONE HMFB

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