SAXSdb — 2nbu

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

UV excision repair protein RAD23

Saccharomyces cerevisiae S288c

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 1–78	Fragment：residues 1-78	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6.5；298 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR sample composition：0.7 mM [U-100% 13C; U-100% 15N] shuttling protein, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 0.1 % sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition：0.7 mM [U-100% 13C; U-100% 15N] shuttling protein, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 0.1 % sodium azide, 100% D2O \| 100% D2O	Resolution not provided

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 2NBU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1X3W Structure of a peptide:N-glycanase-Rad23 complex Deposited 2005-05-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 238–309（72 aa） Fragment：XPC binding domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；sodium chloride, MES, pH 6, VAPOR DIFFUSION, temperature 291K	Resolution 3.00 Å R-free 0.274
1X3Z Structure of a peptide:N-glycanase-Rad23 complex Deposited 2005-05-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 238–309（72 aa） Fragment：XPC binding domain	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；sodium chloride, MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.270
2NBW Solution structure of the Rpn1 T1 site with the Rad23 UBL domain Deposited 2016-03-14	Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–78（78 aa） Fragment：residues 1-78	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.7；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient NMR sample composition 0.3 mM [U-100% 15N] protein_1, 0.04-1.2 mM protein_2, 50 mM HEPES, 50 mM sodium chloride, 1 mM EDTA, 2 mM DTT, 0.1 % sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.04-0.6 mM protein_1, 0.3 mM [U-100% 15N] protein_2, 50 mM HEPES, 50 mM sodium chloride, 1 mM EDTA, 2 mM DTT, 0.1 % sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.6 mM [U-13C] protein_1, 0.6 mM protein_2, 50 mM HEPES, 50 mM sodium chloride, 1 mM EDTA, 2 mM DTT, 0.1 % sodium azide, 100% D2O \| 100% D2O NMR sample composition 0.6 mM protein_1, 0.6 mM [U-13C] protein_2, 50 mM HEPES, 50 mM sodium chloride, 1 mM EDTA, 2 mM DTT, 0.1 % sodium azide, 100% D2O \| 100% D2O	Resolution not provided
2QSF Crystal structure of the Rad4-Rad23 complex Deposited 2007-07-31	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain X 230–398（169 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；100 mM sodium phosphate, 8% (w/v) PEG 2000, 2 mM dithiothreitol, pH 6.5, hanging-drop vapor diffusion, temperature 277K, VAPOR DIFFUSION, HANGING DROP	Resolution 2.35 Å R-free 0.245
2QSG Crystal structure of Rad4-Rad23 bound to a UV-damaged DNA Deposited 2007-07-31	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain X 230–398（169 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；50 mM bis-tris propane, 100mM sodium chloride, 6% (v/v) isopropanol, 14 mM calcium chloride and 5 mM dithiothreitol, pH 6.8, hanging-drop vapor diffusion, temperature 277K, VAPOR DIFFUSION, HANGING DROP	Resolution 3.10 Å R-free 0.277
2QSH Crystal structure of Rad4-Rad23 bound to a mismatch DNA Deposited 2007-07-31	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain X 230–398（169 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；50 mM bis-tris propane, 100 mM sodium chloride, 15% (v/v) isopropanol, 10 mM calcium chloride and 5 mM dithiothreitol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.81 Å R-free 0.244
3ESW Complex of yeast PNGase with GlcNAc2-IAc. Deposited 2008-10-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 254–308（55 aa） Fragment：XPCB Domain	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.5；291 K；0.1 M Tris-HCl, pH 8.5 and 2.0 M sodium chloride, EVAPORATION, temperature 291K	Resolution 3.40 Å R-free 0.235
3M62 Crystal structure of Ufd2 in complex with the ubiquitin-like (UBL) domain of Rad23 Deposited 2010-03-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–84（84 aa） Fragment：UNP residues 1-84, Ubiquitin-like domain	Not recorded	1PE PENTAETHYLENE GLYCOL × 1 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；298 K；16-18% PEG 3500 200 mM Tripotassium citrate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.257
4YIR Crystal structure of Rad4-Rad23 crosslinked to an undamaged DNA Deposited 2015-03-02	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain X 230–398（169 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；50mM BTP-HCl, 100mM NaCl, 14% isopropanol and 100mM calcium chloride	Resolution 3.05 Å R-free 0.253
6CFI Crystal structure of Rad4-Rad23 bound to a 6-4 photoproduct UV lesion Deposited 2018-02-15	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain X 230–398（169 aa） Fragment：residues 230-398	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；bis-tris propane 5 mM sodium chloride 100 mM 1-propanol 14% spermidine-HCl 5 mM dithiothreitol 5 mM	Resolution 3.36 Å R-free 0.268
6UBF Role of Beta-hairpin motifs in the DNA duplex opening by the Rad4/XPC nucleotide excision repair complex Deposited 2019-09-11	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain X 230–398（169 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；50 mM BTP-HCl, 150 mM sodium chloride, 12% isopropanol	Resolution 4.60 Å R-free 0.356
6UG1 Sequence impact in DNA duplex opening by the Rad4/XPC nucleotide excision repair complex Deposited 2019-09-25	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain X 256–311（56 aa） Fragment：UNP residues 256-311	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；50 mM BTP-HCl, 150 mM sodium chloride, 12% isopropanol, 100 mM calcium chloride	Resolution 2.83 Å R-free 0.272
6UIN Role of Beta-hairpin motifs in the DNA duplex opening by the Rad4/XPC nucleotide excision repair complex Deposited 2019-10-01	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain X 230–398（169 aa） Fragment：UNP residues 230-398	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；50 mM BTP-HCl, 200 mM sodium chloride, 12% isopropanol, 100 mM calcium chloride	Resolution 3.35 Å R-free 0.262

13 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RAD23_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–78； UniProt 1–78

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	2nbu
Deposition date deposition_date	2016-03-12
Structure title title	Solution structure of the Rad23 ubiquitin-like (UBL) domain
Keywords keywords	DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	12.24 Å
Radius of gyration Rg (electron density) rg_electron	11.96 Å
Forward intensity I(0) i0	391704000.00
Molecular weight molecular_weight	173680.0 kDa
Excluded volume excluded_volume	220570 Å³
Envelope volume envelope_volume	19653 Å³
Hydration-shell volume shell_volume	11827 Å³
Envelope diameter envelope_diameter	50.5 Å
Shell Rg shell_rg	20.11 Å
Envelope Rg envelope_rg	15.29 Å
Shape Rg shape_rg	11.91 Å
Total Rg total_rg	12.32 Å
Total atoms total_atoms	24940
Residues n_residues	1560
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	45.2 Å
Rg (real space) rg_real	12.21 Å
Rg uncertainty (real space) rg_real_error	0.43 Å
I(0) (real space) i0_real	3.9170e+08
I(0) uncertainty (real space) i0_real_error	4.6270e+06
Rg (reciprocal space) rg_reciprocal	12.21 Å
I(0) (reciprocal space) i0_reciprocal	391700000.0000
Solution quality estimate total_estimate	0.7912
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.5 Å
Skewness Skewness skewness	0.278
Kurtosis Kurtosis kurtosis	0.220
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	126400.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.433; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.997

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2nbua_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id	2nbuA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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8. Citations (1)

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Description description	UV excision repair protein RAD23
Molecular weight formula_weight	11039.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	24940

来源生物 organism	Saccharomyces cerevisiae S288c
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/nb/2nbu/2nbu.fit
pddf	/app/data/pr_computation/nb/2nbu/2nbu.pr.out
profile	/app/data/saxs_computation/nb/2nbu/2nbu.dat

Solution structure of the Rad23 ubiquitin-like (UBL) domain

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

UV excision repair protein RAD23

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)