6w2g

Crystal Structure of Y188G Variant of the Internal UBA Domain of HHR23A in Monoclinic Unit Cell

Method: X-RAY DIFFRACTION Dmax: 52.8 Å Quality: GOOD

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

UV excision repair protein RAD23 homolog A

Homo sapiens

UniProt P54725

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 155–204 Mutation:Y188G EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2M Ammonium sulfate, 0.1M Phosphate-citrate pH 4.2, 40%(v/v) Ethylene glycol Resolution 1.10 Å R-free 0.153
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 155–204 Mutation:Y188G EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2M Ammonium sulfate, 0.1M Phosphate-citrate pH 4.2, 40%(v/v) Ethylene glycol Resolution 1.10 Å R-free 0.153

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.

16 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RD23A_HUMAN
Isoform P54725-2
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–51; UniProt 155–204 Author chain B; PDBConstruct 2–51; UniProt 155–204

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 6w2g

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6w2g
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6w2g
Deposition date deposition_date2020-03-05
Structure title titleCrystal Structure of Y188G Variant of the Internal UBA Domain of HHR23A in Monoclinic Unit Cell
Keywords keywordsUbiquitin Associated Domain, UBA Domain, DNA Binding Protein, Helical Bundle; DNA BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier15.38
Radius of gyration Rg (electron density) rg_electron14.35
Forward intensity I(0) i02635630.00
Molecular weight molecular_weight10851.0 kDa
Excluded volume excluded_volume13469 ų
Envelope volume envelope_volume16329 ų
Hydration-shell volume shell_volume10201 ų
Envelope diameter envelope_diameter50.6
Shell Rg shell_rg19.24
Envelope Rg envelope_rg14.71
Shape Rg shape_rg14.35
Total Rg total_rg15.44
Total atoms total_atoms1446
Residues n_residues97
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 dmax52.8
Rg (real space) rg_real15.39
Rg uncertainty (real space) rg_real_error0.43
I(0) (real space) i0_real2.6360e+06
I(0) uncertainty (real space) i0_real_error3.2940e+04
Rg (reciprocal space) rg_reciprocal15.39
I(0) (reciprocal space) i0_reciprocal2636000.0000
Solution quality estimate total_estimate0.8489
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary16.1
Skewness Skewness skewness0.357
Kurtosis Kurtosis kurtosis-0.295
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha777600.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.702; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.943; Smooth: 0.982

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6w2ga_
Class classa — All alpha proteins
Fold Fold folda.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamilya.5.2 — UBA-like
Family Family familya.5.2.1 — UBA domain
Domain ID domain_idd6w2gb_
Class classa — All alpha proteins
Fold Fold folda.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamilya.5.2 — UBA-like
Family Family familya.5.2.1 — UBA domain

8. Citations (1)

9. Files and Curves (10)