SAXSdb — 1b8z

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

PROTEIN (HISTONELIKE PROTEIN HU)

Thermotoga maritima

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 1–90 Chain B； UniProt 1–90	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.6；pH 4.6	Resolution 1.60 Å R-free 0.236

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 1B8Z	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1RIY HU mutant V42I from Thermotoga maritima Deposited 2003-11-18	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–90（90 aa）	Mutation：V42I	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.3；293 K；100mM Na-acetate, pH 4.0-4.5, 80-90% saturated ammonium sulphate, pH 4.3, VAPOR DIFFUSION, temperature 293K	Resolution 1.80 Å R-free 0.286

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

View Construct and Data Evidence

UniProt name	DBH_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–90； UniProt 1–90 Author chain B； PDBConstruct 1–90； UniProt 1–90

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	1b8z
Deposition date deposition_date	1999-02-03
Structure title title	HU FROM THERMOTOGA MARITIMA
Keywords keywords	THERMOTOGA MARITIMA, THERMOSTABLE DNA BINDING PROTEIN, DNA BINDING PROTEIN; DNA BINDING PROTEIN
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	15.73 Å
Radius of gyration Rg (electron density) rg_electron	14.16 Å
Forward intensity I(0) i0	3603130.00
Molecular weight molecular_weight	14806.0 kDa
Excluded volume excluded_volume	19379 Å³
Envelope volume envelope_volume	22075 Å³
Hydration-shell volume shell_volume	13066 Å³
Envelope diameter envelope_diameter	47.4 Å
Shell Rg shell_rg	20.14 Å
Envelope Rg envelope_rg	14.50 Å
Shape Rg shape_rg	14.10 Å
Total Rg total_rg	15.78 Å
Total atoms total_atoms	1040
Residues n_residues	134
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	48.1 Å
Rg (real space) rg_real	15.59 Å
Rg uncertainty (real space) rg_real_error	0.26 Å
I(0) (real space) i0_real	3.6030e+06
I(0) uncertainty (real space) i0_real_error	3.8110e+04
Rg (reciprocal space) rg_reciprocal	15.60 Å
I(0) (reciprocal space) i0_reciprocal	3603000.0000
Solution quality estimate total_estimate	0.8902
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.5 Å
Skewness Skewness skewness	-0.007
Kurtosis Kurtosis kurtosis	-0.438
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	696000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.865; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.990

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1b8za_
Class class	a — All alpha proteins
Fold Fold fold	a.55 — IHF-like DNA-binding proteins
Superfamily Superfamily superfamily	a.55.1 — IHF-like DNA-binding proteins
Family Family family	a.55.1.1 — Prokaryotic DNA-bending protein

Domain ID domain_id	d1b8zb_
Class class	a — All alpha proteins
Fold Fold fold	a.55 — IHF-like DNA-binding proteins
Superfamily Superfamily superfamily	a.55.1 — IHF-like DNA-binding proteins
Family Family family	a.55.1.1 — Prokaryotic DNA-bending protein

CATH v4.4 (2 domains)

Domain ID domain_id	1b8zA00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	520 — HU Protein; Chain A
Homologous superfamily homologous superfamily	10 — IHF-like DNA-binding proteins

Domain ID domain_id	1b8zB00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	520 — HU Protein; Chain A
Homologous superfamily homologous superfamily	10 — IHF-like DNA-binding proteins

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8. Citations (1)

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Unit-cell length a length_a	46.120 Å
Unit-cell length b length_b	46.120 Å
Unit-cell length c length_c	77.560 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	8

Space group space_group	P 43
Space-group number int_tables_number	78
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	—
R_work r_work	0.2150
R_free r_free	0.2360

Description description	PROTEIN (HISTONELIKE PROTEIN HU)
Molecular weight formula_weight	10018.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1117

HU FROM THERMOTOGA MARITIMA

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

PROTEIN (HISTONELIKE PROTEIN HU)

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Thermotoga maritima
NCBI Class编号 ncbi_taxonomy_id	2336
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	77

fit	/app/data/saxs_computation/b8/1b8z/1b8z.fit
pddf	/app/data/pr_computation/b8/1b8z/1b8z.pr.out
profile	/app/data/saxs_computation/b8/1b8z/1b8z.dat