2qld

human Hsp40 Hdj1

Method: X-RAY DIFFRACTION Dmax: 92.8 Å Quality: REASONABLE

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

DnaJ homolog subfamily B member 1

Homo sapiens

UniProt P25685

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 158–340 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.5;295 K;100mM Citric buffer, PEG400 25%, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.70 Å R-free 0.336

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.

14 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DNJB1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–183; UniProt 158–340

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.

SAXS scattering curve SAXS Profile

SAXS profile for 2qld

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2qld
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2qld
Deposition date deposition_date2007-07-12
Structure title titlehuman Hsp40 Hdj1
Keywords keywordsprimarily beta sheets, CHAPERONE; CHAPERONE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier24.58
Radius of gyration Rg (electron density) rg_electron24.72
Forward intensity I(0) i06400370.00
Molecular weight molecular_weight19326.0 kDa
Excluded volume excluded_volume24562 ų
Envelope volume envelope_volume31894 ų
Hydration-shell volume shell_volume13046 ų
Envelope diameter envelope_diameter96.4
Shell Rg shell_rg26.78
Envelope Rg envelope_rg25.62
Shape Rg shape_rg24.68
Total Rg total_rg25.14
Total atoms total_atoms1359
Residues n_residues171
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax92.8
Rg (real space) rg_real25.21
Rg uncertainty (real space) rg_real_error1.12
I(0) (real space) i0_real6.4000e+06
I(0) uncertainty (real space) i0_real_error9.6820e+04
Rg (reciprocal space) rg_reciprocal25.06
I(0) (reciprocal space) i0_reciprocal6400000.0000
Solution quality estimate total_estimate0.6992
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary17.7
Skewness Skewness skewness0.697
Kurtosis Kurtosis kurtosis-0.127
Angular range angular_range— – 0.3250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha822600.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.367; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.055; Smooth: 0.929

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2qlda1
Class classb — All beta proteins
Fold Fold foldb.4 — HSP40/DnaJ peptide-binding domain
Superfamily Superfamily superfamilyb.4.1 — HSP40/DnaJ peptide-binding domain
Family Family familyb.4.1.0 — automated matches
Domain ID domain_idd2qlda2
Class classb — All beta proteins
Fold Fold foldb.4 — HSP40/DnaJ peptide-binding domain
Superfamily Superfamily superfamilyb.4.1 — HSP40/DnaJ peptide-binding domain
Family Family familyb.4.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id2qldA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology260 — HSP40/DNAj peptide-binding domain
Homologous superfamily homologous superfamily20 — Urease metallochaperone UreE, N-terminal domain
Domain ID domain_id2qldA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology260 — HSP40/DNAj peptide-binding domain
Homologous superfamily homologous superfamily20 — Urease metallochaperone UreE, N-terminal domain

8. Citations (1)

9. Files and Curves (10)