SAXSdb — 1xqr

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

HspBP1 protein

Homo sapiens

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 84–359	Fragment：core domain (residues 84-359) Mutation：E88G Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：MICROBATCH；pH 8.5；293 K；PEGMME2000, Potassium Acetate, Glycerol, iso-propanol, EDTA, TCEP, Tris-HCl, pH 8.5, microbatch, temperature 293K	Resolution 2.10 Å R-free 0.249
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 84–359	Fragment：core domain (residues 84-359) Mutation：E88G Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：MICROBATCH；pH 8.5；293 K；PEGMME2000, Potassium Acetate, Glycerol, iso-propanol, EDTA, TCEP, Tris-HCl, pH 8.5, microbatch, temperature 293K	Resolution 2.10 Å R-free 0.249

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 1XQR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1XQS Crystal structure of the HspBP1 core domain complexed with the fragment of Hsp70 ATPase domain Deposited 2004-10-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 84–359（276 aa） Fragment：core domain (84-359)	Mutation：E88G	AMP ADENOSINE MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG8000, Potassium chloride, Magnesium chloride, AMP-PNP, DTT, HEPES KOH, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.90 Å R-free 0.296
1XQS Crystal structure of the HspBP1 core domain complexed with the fragment of Hsp70 ATPase domain Deposited 2004-10-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 84–359（276 aa） Fragment：core domain (84-359)	Mutation：E88G	AMP ADENOSINE MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG8000, Potassium chloride, Magnesium chloride, AMP-PNP, DTT, HEPES KOH, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.90 Å R-free 0.296
8X87 The Crystal Structure of HspBP1 from Biortus. Deposited 2023-11-27	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 84–359（276 aa）	Mutation：E88G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20mM Tris-HCl (pH 8.0), 100mM NaCl, 1mM MgCl2	Resolution 2.20 Å R-free 0.249
8X87 The Crystal Structure of HspBP1 from Biortus. Deposited 2023-11-27	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 84–359（276 aa）	Mutation：E88G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20mM Tris-HCl (pH 8.0), 100mM NaCl, 1mM MgCl2	Resolution 2.20 Å R-free 0.249
8X87 The Crystal Structure of HspBP1 from Biortus. Deposited 2023-11-27	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 84–359（276 aa）	Mutation：E88G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20mM Tris-HCl (pH 8.0), 100mM NaCl, 1mM MgCl2	Resolution 2.20 Å R-free 0.249
8X87 The Crystal Structure of HspBP1 from Biortus. Deposited 2023-11-27	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 84–359（276 aa）	Mutation：E88G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20mM Tris-HCl (pH 8.0), 100mM NaCl, 1mM MgCl2	Resolution 2.20 Å R-free 0.249

2 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HPBP1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–296； UniProt 84–359 Author chain B； PDBConstruct 21–296； UniProt 84–359

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	1xqr
Deposition date deposition_date	2004-10-13
Structure title title	Crystal structure of the HspBP1 core domain
Keywords keywords	armadillo repeat, superhelical twist, CHAPERONE; CHAPERONE
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	28.68 Å
Radius of gyration Rg (electron density) rg_electron	27.81 Å
Forward intensity I(0) i0	64185400.00
Molecular weight molecular_weight	59869.0 kDa
Excluded volume excluded_volume	73601 Å³
Envelope volume envelope_volume	93989 Å³
Hydration-shell volume shell_volume	28803 Å³
Envelope diameter envelope_diameter	95.7 Å
Shell Rg shell_rg	34.02 Å
Envelope Rg envelope_rg	27.82 Å
Shape Rg shape_rg	27.76 Å
Total Rg total_rg	28.57 Å
Total atoms total_atoms	4118
Residues n_residues	518
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	91.7 Å
Rg (real space) rg_real	28.70 Å
Rg uncertainty (real space) rg_real_error	0.76 Å
I(0) (real space) i0_real	6.4190e+07
I(0) uncertainty (real space) i0_real_error	9.2660e+05
Rg (reciprocal space) rg_reciprocal	28.69 Å
I(0) (reciprocal space) i0_reciprocal	64180000.0000
Solution quality estimate total_estimate	0.8899
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	90.0 Å
Skewness Skewness skewness	0.340
Kurtosis Kurtosis kurtosis	-0.387
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13140000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.936; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.954; Smooth: 0.802

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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) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1xqra1
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.1 — ARM repeat
Family Family family	a.118.1.21 — HspBP1 domain

Domain ID domain_id	d1xqra2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1xqrb2
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.1 — ARM repeat
Family Family family	a.118.1.21 — HspBP1 domain

Domain ID domain_id	d1xqrb3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	1xqrA00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily	10 — Leucine-rich Repeat Variant

Domain ID domain_id	1xqrB00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily	10 — Leucine-rich Repeat Variant

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8. Citations (1)

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Unit-cell length a length_a	76.680 Å
Unit-cell length b length_b	84.286 Å
Unit-cell length c length_c	89.945 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	38.070 Å
R factor r_factor	0.2130
R_work r_work	0.2110
R_free r_free	0.2488

Description description	HspBP1 protein
Molecular weight formula_weight	33528.9 kDa
Mutation mutation	E88G
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	4262

Crystal structure of the HspBP1 core domain

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

HspBP1 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) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
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	144

fit	/app/data/saxs_computation/xq/1xqr/1xqr.fit
pddf	/app/data/pr_computation/xq/1xqr/1xqr.pr.out
profile	/app/data/saxs_computation/xq/1xqr/1xqr.dat