SAXSdb — 1ud0

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

70 kDa heat-shock-like 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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 542–646 Chain B； UniProt 542–646	Fragment：C-TERMINAL SUBDOMAIN Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.9；298 K；ammonium sulfate, 2-propanol, sodium acetate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.45 Å R-free 0.309
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 542–646 Chain D； UniProt 542–646	Fragment：C-TERMINAL SUBDOMAIN Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.9；298 K；ammonium sulfate, 2-propanol, sodium acetate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.45 Å R-free 0.309
3	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 542–646 Chain B； UniProt 542–646 Chain C； UniProt 542–646 Chain D； UniProt 542–646	Fragment：C-TERMINAL SUBDOMAIN Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.9；298 K；ammonium sulfate, 2-propanol, sodium acetate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.45 Å R-free 0.309
4	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 542–646 Chain B； UniProt 542–646 Chain C； UniProt 542–646 Chain D； UniProt 542–646	Fragment：C-TERMINAL SUBDOMAIN Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.9；298 K；ammonium sulfate, 2-propanol, sodium acetate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.45 Å R-free 0.309

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 1UD0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CKR HIGH RESOLUTION SOLUTION STRUCTURE OF THE HEAT SHOCK COGNATE-70 KD SUBSTRATE BINDING DOMAIN OBTAINED BY MULTIDIMENSIONAL NMR TECHNIQUES Deposited 1999-04-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 385–542（158 aa） Fragment：SUBSTRATE BINDING DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 50 mM SODIUM PHOSPHATE；Pressure 1 NMR sample composition 1.5 MM 15N OR 15N,13C LABELED PROTEIN 5%D20/95%H2O AND 100%D2O	Resolution not provided
7HSC HIGH RESOLUTION SOLUTION STRUCTURE OF THE HEAT SHOCK COGNATE-70 KD SUBSTRATE BINDING DOMAIN OBTAINED BY MULTIDIMENSIONAL NMR TECHNIQUES Deposited 1999-05-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 385–543（159 aa） Fragment：SUBSTRATE BINDING DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 50 mM SODIUM PHOSPHATE；Pressure 1 NMR sample composition 1.5 MM 15N OR 15N,13C LABELED PROTEIN 5%D20/95%H2O AND 100%D2O	Resolution not provided

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

View Construct and Data Evidence

UniProt name	HSP7C_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–113； UniProt 542–646 Author chain B； PDBConstruct 9–113； UniProt 542–646 Author chain C； PDBConstruct 9–113； UniProt 542–646 Author chain D； PDBConstruct 9–113； UniProt 542–646

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	1ud0
Deposition date deposition_date	2003-04-24
Structure title title	CRYSTAL STRUCTURE OF THE C-TERMINAL 10-kDA SUBDOMAIN OF HSC70
Keywords keywords	HSC70, 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	28.26 Å
Radius of gyration Rg (electron density) rg_electron	27.98 Å
Forward intensity I(0) i0	27904100.00
Molecular weight molecular_weight	38945.0 kDa
Excluded volume excluded_volume	47806 Å³
Envelope volume envelope_volume	64896 Å³
Hydration-shell volume shell_volume	21149 Å³
Envelope diameter envelope_diameter	96.1 Å
Shell Rg shell_rg	32.08 Å
Envelope Rg envelope_rg	28.37 Å
Shape Rg shape_rg	27.89 Å
Total Rg total_rg	28.69 Å
Total atoms total_atoms	2682
Residues n_residues	320
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	90.1 Å
Rg (real space) rg_real	28.35 Å
Rg uncertainty (real space) rg_real_error	0.76 Å
I(0) (real space) i0_real	2.7900e+07
I(0) uncertainty (real space) i0_real_error	4.1370e+05
Rg (reciprocal space) rg_reciprocal	28.33 Å
I(0) (reciprocal space) i0_reciprocal	27900000.0000
Solution quality estimate total_estimate	0.8852
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	37.0 Å
Skewness Skewness skewness	0.257
Kurtosis Kurtosis kurtosis	-0.686
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3443000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.824; Smooth: 0.874

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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	70 kDa heat-shock-like protein
Molecular weight formula_weight	12450.3 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	2705

LVPRGSHMLESYAFNMKATVEDEKLQGKINDEDKQKILDKCNEIISWLDKNQTAEKEEFEHQQKELEKVCNPIITKLYQSAGGMPGGMPGGFPGGGAPPSGGASSGPTIEEVD

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	23

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1ud0a1
Class class	a — All alpha proteins
Fold Fold fold	a.8 — immunoglobulin/albumin-binding domain-like
Superfamily Superfamily superfamily	a.8.4 — Heat shock protein 70kD (HSP70), C-terminal subdomain
Family Family family	a.8.4.1 — Heat shock protein 70kD (HSP70), C-terminal subdomain

Domain ID domain_id	d1ud0a2
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	d1ud0b1
Class class	a — All alpha proteins
Fold Fold fold	a.8 — immunoglobulin/albumin-binding domain-like
Superfamily Superfamily superfamily	a.8.4 — Heat shock protein 70kD (HSP70), C-terminal subdomain
Family Family family	a.8.4.1 — Heat shock protein 70kD (HSP70), C-terminal subdomain

Domain ID domain_id	d1ud0b2
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	d1ud0c1
Class class	a — All alpha proteins
Fold Fold fold	a.8 — immunoglobulin/albumin-binding domain-like
Superfamily Superfamily superfamily	a.8.4 — Heat shock protein 70kD (HSP70), C-terminal subdomain
Family Family family	a.8.4.1 — Heat shock protein 70kD (HSP70), C-terminal subdomain

Domain ID domain_id	d1ud0c2
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	d1ud0d1
Class class	a — All alpha proteins
Fold Fold fold	a.8 — immunoglobulin/albumin-binding domain-like
Superfamily Superfamily superfamily	a.8.4 — Heat shock protein 70kD (HSP70), C-terminal subdomain
Family Family family	a.8.4.1 — Heat shock protein 70kD (HSP70), C-terminal subdomain

Domain ID domain_id	d1ud0d2
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 (4 domains)

Domain ID domain_id	1ud0A01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1ud0B01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1ud0C01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1ud0D01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	10 —

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8. Citations (1)

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Unit-cell length a length_a	117.479 Å
Unit-cell length b length_b	117.479 Å
Unit-cell length c length_c	163.777 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	48

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	3.450 Å
Low-resolution limit resolution_low	14.930 Å
R factor r_factor	0.2490
R_work r_work	0.2490
R_free r_free	0.3090

fit	/app/data/saxs_computation/ud/1ud0/1ud0.fit
pddf	/app/data/pr_computation/ud/1ud0/1ud0.pr.out
profile	/app/data/saxs_computation/ud/1ud0/1ud0.dat

CRYSTAL STRUCTURE OF THE C-TERMINAL 10-kDA SUBDOMAIN OF HSC70

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

70 kDa heat-shock-like 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