SAXSdb — 1riy

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

Hu DNA-binding protein

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	Mutation：V42I	No other associated polymer	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

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 1RIY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B8Z HU FROM THERMOTOGA MARITIMA Deposited 1999-02-03	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） Chain B 1–90（90 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；pH 4.6	Resolution 1.60 Å R-free 0.236

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

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	1riy
Deposition date deposition_date	2003-11-18
Structure title title	HU mutant V42I from Thermotoga maritima
Keywords keywords	HISTONE-LIKE PROTEIN, THERMOSTABLE DNA-BINDING PROTEIN, HU PROTEIN MUTANT V42I, THERMOTOGA MARITIMA, 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	15.58 Å
Radius of gyration Rg (electron density) rg_electron	14.18 Å
Forward intensity I(0) i0	1000270.00
Molecular weight molecular_weight	7333.0 kDa
Excluded volume excluded_volume	9565 Å³
Envelope volume envelope_volume	12069 Å³
Hydration-shell volume shell_volume	7708 Å³
Envelope diameter envelope_diameter	47.9 Å
Shell Rg shell_rg	18.72 Å
Envelope Rg envelope_rg	14.14 Å
Shape Rg shape_rg	14.15 Å
Total Rg total_rg	15.53 Å
Total atoms total_atoms	517
Residues n_residues	71
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	49.1 Å
Rg (real space) rg_real	15.52 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	1.0000e+06
I(0) uncertainty (real space) i0_real_error	1.1340e+04
Rg (reciprocal space) rg_reciprocal	15.53 Å
I(0) (reciprocal space) i0_reciprocal	1000000.0000
Solution quality estimate total_estimate	0.8776
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.2 Å
Skewness Skewness skewness	-0.042
Kurtosis Kurtosis kurtosis	-0.697
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	67490.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.834; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.955; Smooth: 0.948

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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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1riya_
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 (1 domains)

Domain ID domain_id	1riyA00
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	45.447 Å
Unit-cell length b length_b	45.447 Å
Unit-cell length c length_c	76.204 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 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	15.870 Å
R factor r_factor	0.2192
R_work r_work	0.2162
R_free r_free	0.2859

Description description	Hu DNA-binding protein
Molecular weight formula_weight	10032.1 kDa
Mutation mutation	V42I
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	552

HU mutant V42I from Thermotoga maritima

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

Hu DNA-binding protein

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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 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 BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	35

fit	/app/data/saxs_computation/ri/1riy/1riy.fit
pddf	/app/data/pr_computation/ri/1riy/1riy.pr.out
profile	/app/data/saxs_computation/ri/1riy/1riy.dat