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4q0z

The catalytic core of Rad2 in complex with DNA substrate (complex III)

Method: X-RAY DIFFRACTION Dmax: 131.7 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Rad2p

Saccharomyces cerevisiae

UniProt P07276

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–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain A； UniProt 2–111 Chain A； UniProt 732–986 Chain B； UniProt 2–111 Chain B； UniProt 732–986 Fragment：Rad2 catalytic core ;DNA (5'-D(*TP*GP*CP*TP*CP*CP*CP*TP*TP*GP*TP*CP*TP*CP*AP*GP*T)-3') ; × 1 ;DNA (5'-D(*TP*CP*TP*GP*AP*GP*AP*CP*AP*AP*GP*GP*GP*AP*GP*CP*T)-3') ; × 1 CA CALCIUM ION × 2 K POTASSIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；10% (w/v) PEG 8000, 20% (v/v) ethylene glycol, 0.2 M D-glucose, 0.2 M D-mannose, 0.2 M D-galactose, 0.2 M L-fructose, 0.2 M D-xylose, 0.2 M N-acetyl-D-glucosamine, and 0.1 M MES/imidazole, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K Resolution 2.40 Å R-free 0.235
2 Protein–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain E； UniProt 2–111 Chain E； UniProt 732–986 Chain F； UniProt 2–111 Chain F； UniProt 732–986 Fragment：Rad2 catalytic core ;DNA (5'-D(*TP*GP*CP*TP*CP*CP*CP*TP*TP*GP*TP*CP*TP*CP*AP*GP*T)-3') ; × 1 ;DNA (5'-D(*TP*CP*TP*GP*AP*GP*AP*CP*AP*AP*GP*GP*GP*AP*GP*CP*T)-3') ; × 1 CA CALCIUM ION × 2 K POTASSIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；10% (w/v) PEG 8000, 20% (v/v) ethylene glycol, 0.2 M D-glucose, 0.2 M D-mannose, 0.2 M D-galactose, 0.2 M L-fructose, 0.2 M D-xylose, 0.2 M N-acetyl-D-glucosamine, and 0.1 M MES/imidazole, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K Resolution 2.40 Å R-free 0.235

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 4Q0Z Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2LOX NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and Rad2 Deposited 2012-01-27 Different construct Different mutation/modification 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 642–690（49 aa） Fragment：UNP residues 642-690
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；300 K；Pressure ambient
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Tfb1, 1.25 mM Rad2, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Tfb1, 1.25 mM Rad2, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 100% D2O | 100% D2O
NMR sample composition 1 mM [U-100% 15N] Tfb1, 1.25 mM Rad2, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1.25 mM Tfb1, 1 mM [U-100% 13C; U-100% 15N] Rad2, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1.25 mM Tfb1, 1 mM [U-100% 13C; U-100% 15N] Rad2, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 100% D2O | 100% D2O
NMR sample composition 1.25 mM Tfb1, 1 mM [U-100% 15N] Rad2, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
4Q0R The catalytic core of Rad2 (complex I) Deposited 2014-04-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric
Chain A 2–111（110 aa） Fragment：enzyme catalytic core, unp residues 2-111, unp residues 732-986
Chain A 732–986（255 aa） Fragment：enzyme catalytic core, unp residues 2-111, unp residues 732-986
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% (v/v) ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.75 Å R-free 0.310
4Q0R The catalytic core of Rad2 (complex I) Deposited 2014-04-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–111（110 aa） Fragment：enzyme catalytic core, unp residues 2-111, unp residues 732-986
Chain B 732–986（255 aa） Fragment：enzyme catalytic core, unp residues 2-111, unp residues 732-986
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% (v/v) ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.75 Å R-free 0.310
4Q0W he catalytic core of Rad2 in complex with DNA substrate (complex II) Deposited 2014-04-02 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 2–111（110 aa） Fragment：Rad2
Chain A 732–986（255 aa） Fragment：Rad2
Chain B 2–111（110 aa） Fragment：Rad2
Chain B 732–986（255 aa） Fragment：Rad2
Not recorded CA CALCIUM ION × 2 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；9% (w/v) PEG 20000, 20% (v/v) PEG MME 550, 0.2 M D-glucose, 0.2 M D-mannose, 0.2 M D-galactose, 0.2 M L-fructose, 0.2 M D-xylose, 0.2 M N-acetyl-D-glucosamine, and 0.1 M MOPS/HEPES-Na, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.10 Å R-free 0.230
4Q10 The catalytic core of Rad2 in complex with DNA substrate (complex IV) Deposited 2014-04-02 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 2–111（110 aa） Fragment：enzyme catalytic core, unp residues 2-111, unp residues 732-986
Chain A 732–986（255 aa） Fragment：enzyme catalytic core, unp residues 2-111, unp residues 732-986
Chain B 2–111（110 aa） Fragment：enzyme catalytic core, unp residues 2-111, unp residues 732-986
Chain B 732–986（255 aa） Fragment：enzyme catalytic core, unp residues 2-111, unp residues 732-986
Not recorded CA CALCIUM ION × 2 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；8% (w/v) PEG 8000, 18% (v/v) ethylene glycol, 0.2 M D-glucose, 0.2 M D-mannose, 0.2 M D-galactose, 0.2 M L-fructose, 0.2 M D-xylose, 0.2 M N-acetyl-D-glucosamine, and 0.1 M MOPS/HEPES-Na, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.70 Å R-free 0.284

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RAD2_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–110； UniProt 2–111 Author chain A； PDBConstruct 111–365； UniProt 732–986 Author chain B； PDBConstruct 1–110； UniProt 2–111 Author chain B； PDBConstruct 111–365； UniProt 732–986 Author chain E； PDBConstruct 1–110； UniProt 2–111 Author chain E； PDBConstruct 111–365； UniProt 732–986 Author chain F； PDBConstruct 1–110； UniProt 2–111 Author chain F； PDBConstruct 111–365； UniProt 732–986

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 4q0z

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4q0z
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4q0z
Deposition date deposition_date2014-04-02
Structure title titleThe catalytic core of Rad2 in complex with DNA substrate (complex III)
Keywords keywordsba Rossmann-like, DNA repair, TFIIH, Hydrolase-DNA complex; Hydrolase/DNA
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier40.82 Å
Radius of gyration Rg (electron density) rg_electron41.43 Å
Forward intensity I(0) i0430389000.00
Molecular weight molecular_weight160730.0 kDa
Excluded volume excluded_volume197070 ų
Envelope volume envelope_volume282120 ų
Hydration-shell volume shell_volume58227 ų
Envelope diameter envelope_diameter140.8 Å
Shell Rg shell_rg45.86 Å
Envelope Rg envelope_rg40.17 Å
Shape Rg shape_rg41.45 Å
Total Rg total_rg41.57 Å
Total atoms total_atoms11234
Residues n_residues1308
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax131.7 Å
Rg (real space) rg_real40.81 Å
Rg uncertainty (real space) rg_real_error0.88 Å
I(0) (real space) i0_real4.3040e+08
I(0) uncertainty (real space) i0_real_error6.7960e+06
Rg (reciprocal space) rg_reciprocal40.82 Å
I(0) (reciprocal space) i0_reciprocal430400000.0000
Solution quality estimate total_estimate0.6689
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary54.0 Å
Skewness Skewness skewness0.323
Kurtosis Kurtosis kurtosis-0.260
Angular range angular_range— – 0.1950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha84840000.0000
Real-space data points n_real_points40
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.906; Stabil: 1.000; Sysdev: 0.107; Positv: 1.000; Valcen: 0.994; Smooth: 0.659
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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8. Citations (1)

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9. Files and Curves (10)