SAXSdb — 4j8e

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

Hsc70-interacting protein

Rattus norvegicus

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 78–247	Fragment：UNP residues 78-247	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；2.3 Na-malonate, pH 6.0, vapor diffusion, hanging drop, temperature 291K	Resolution 2.60 Å R-free 0.248
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 78–247	Fragment：UNP residues 78-247	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；2.3 Na-malonate, pH 6.0, vapor diffusion, hanging drop, temperature 291K	Resolution 2.60 Å R-free 0.248
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 78–247 Chain B； UniProt 78–247	Fragment：UNP residues 78-247	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；2.3 Na-malonate, pH 6.0, vapor diffusion, hanging drop, temperature 291K	Resolution 2.60 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 4J8E	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4J8C Crystal structure of the dimerization domain of Hsc70-interacting protein Deposited 2013-02-14	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–44（44 aa） Fragment：UNP residues 1-44 Chain B 1–44（44 aa） Fragment：UNP residues 1-44	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.52 Na-malonate, pH 7.0, vapor diffusion, hanging drop, temperature 291K	Resolution 1.10 Å R-free 0.162
4J8D Middle domain of Hsc70-interacting protein, crystal form II Deposited 2013-02-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 79–248（170 aa） Fragment：UNP residues 78-247	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.15 Na-malonate, pH 7.0, vapor diffusion, hanging drop, temperature 291K	Resolution 2.80 Å R-free 0.299
4J8D Middle domain of Hsc70-interacting protein, crystal form II Deposited 2013-02-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 79–248（170 aa） Fragment：UNP residues 78-247	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.15 Na-malonate, pH 7.0, vapor diffusion, hanging drop, temperature 291K	Resolution 2.80 Å R-free 0.299
4J8D Middle domain of Hsc70-interacting protein, crystal form II Deposited 2013-02-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 79–248（170 aa） Fragment：UNP residues 78-247	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.15 Na-malonate, pH 7.0, vapor diffusion, hanging drop, temperature 291K	Resolution 2.80 Å R-free 0.299
4J8D Middle domain of Hsc70-interacting protein, crystal form II Deposited 2013-02-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 79–248（170 aa） Fragment：UNP residues 78-247	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.15 Na-malonate, pH 7.0, vapor diffusion, hanging drop, temperature 291K	Resolution 2.80 Å R-free 0.299
4J8F Crystal structure of a fusion protein containing the NBD of Hsp70 and the middle domain of Hip Deposited 2013-02-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 77–247（171 aa） Fragment：P08107 residues 1-382, P50503 residues 77-247	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 PO4 PHOSPHATE ION × 2 IOD IODIDE ION × 34	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；17 % PEG-3350 and 0.2 M NH4I, pH 7.4, vapor diffusion, hanging drop, temperature 291K	Resolution 2.70 Å R-free 0.261
4J8F Crystal structure of a fusion protein containing the NBD of Hsp70 and the middle domain of Hip Deposited 2013-02-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 77–247（171 aa） Fragment：P08107 residues 1-382, P50503 residues 77-247	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 PO4 PHOSPHATE ION × 1 IOD IODIDE ION × 17	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；17 % PEG-3350 and 0.2 M NH4I, pH 7.4, vapor diffusion, hanging drop, temperature 291K	Resolution 2.70 Å R-free 0.261

3 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	F10A1_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–175； UniProt 78–247 Author chain B； PDBConstruct 6–175； UniProt 78–247

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	4j8e
Deposition date deposition_date	2013-02-14
Structure title title	Middle domain of Hsc70-interacting protein, crystal form I
Keywords keywords	tetratricopeptide repeat, solenoid, Co-chaperone, cytosol, 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	22.97 Å
Radius of gyration Rg (electron density) rg_electron	22.22 Å
Forward intensity I(0) i0	13403300.00
Molecular weight molecular_weight	26743.0 kDa
Excluded volume excluded_volume	33243 Å³
Envelope volume envelope_volume	41527 Å³
Hydration-shell volume shell_volume	16918 Å³
Envelope diameter envelope_diameter	79.8 Å
Shell Rg shell_rg	27.31 Å
Envelope Rg envelope_rg	22.47 Å
Shape Rg shape_rg	22.18 Å
Total Rg total_rg	23.06 Å
Total atoms total_atoms	1877
Residues n_residues	238
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	77.7 Å
Rg (real space) rg_real	23.14 Å
Rg uncertainty (real space) rg_real_error	0.63 Å
I(0) (real space) i0_real	1.3400e+07
I(0) uncertainty (real space) i0_real_error	2.0470e+05
Rg (reciprocal space) rg_reciprocal	23.10 Å
I(0) (reciprocal space) i0_reciprocal	13400000.0000
Solution quality estimate total_estimate	0.8442
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.7 Å
Skewness Skewness skewness	0.447
Kurtosis Kurtosis kurtosis	-0.558
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1581000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.745; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.738; Smooth: 0.996

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Hsc70-interacting protein
Molecular weight formula_weight	19761.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1888

GARGGSDLEIDNEGVIEADTDAPQEMGDENAEITEAMMDEANEKKGAAIDALNDGELQKAIDLFTDAIKLNPRLAILYAKRASVFVKLQKPNAAIRDCDRAIEINPDSAQPYKWRGKAHRLLGHWEEAARDLALACKLDYDEDASAMLREVQPRAQKIAEHRRKYERKREEREIK

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	brown rat,rat,rats
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	11

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4j8ea_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.8 — TPR-like
Family Family family	a.118.8.0 — automated matches

Domain ID domain_id	d4j8eb_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.8 — TPR-like
Family Family family	a.118.8.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	4j8eA00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

Domain ID domain_id	4j8eB00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

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8. Citations (1)

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Unit-cell length a length_a	79.856 Å
Unit-cell length b length_b	79.856 Å
Unit-cell length c length_c	97.311 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	16

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1870
R_work r_work	0.1841
R_free r_free	0.2481

fit	/app/data/saxs_computation/j8/4j8e/4j8e.fit
pddf	/app/data/pr_computation/j8/4j8e/4j8e.pr.out
profile	/app/data/saxs_computation/j8/4j8e/4j8e.dat

Middle domain of Hsc70-interacting protein, crystal form I

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

Hsc70-interacting 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