SAXSdb — 4q0r

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

DNA repair protein RAD2

Saccharomyces cerevisiae

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 Monomer Protein × 1 DNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain A； UniProt 2–111 Chain A； UniProt 732–986	Fragment：enzyme catalytic core, unp residues 2-111, unp residues 732-986 Non-standard monomer：Yes (specific site not provided by mmCIF)	;DNA (5'-D(CPTPGPAPGPTPCPAPGPAPGPCPAPAP*A)-3') ; × 1	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 2–111 Chain B； UniProt 732–986	Fragment：enzyme catalytic core, unp residues 2-111, unp residues 732-986 Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	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

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 4Q0R	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 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
4Q0W he catalytic core of Rad2 in complex with DNA substrate (complex II) 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 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
4Q0Z The catalytic core of Rad2 in complex with DNA substrate (complex III) 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 Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–111（110 aa） Fragment：Rad2 catalytic core Chain A 732–986（255 aa） Fragment：Rad2 catalytic core Chain B 2–111（110 aa） Fragment：Rad2 catalytic core Chain B 732–986（255 aa） Fragment：Rad2 catalytic core	Not recorded	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
4Q0Z The catalytic core of Rad2 in complex with DNA substrate (complex III) 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–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain E 2–111（110 aa） Fragment：Rad2 catalytic core Chain E 732–986（255 aa） Fragment：Rad2 catalytic core Chain F 2–111（110 aa） Fragment：Rad2 catalytic core Chain F 732–986（255 aa） Fragment：Rad2 catalytic core	Not recorded	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
4Q10 The catalytic core of Rad2 in complex with DNA substrate (complex IV) 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 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 3–112； UniProt 2–111 Author chain A； PDBConstruct 113–367； UniProt 732–986 Author chain B； PDBConstruct 3–112； UniProt 2–111 Author chain B； PDBConstruct 113–367； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4q0r
Deposition date deposition_date	2014-04-02
Structure title title	The catalytic core of Rad2 (complex I)
Keywords keywords	nuclease, nucleotide excision repair, nucleus, Hydrolase-DNA complex; Hydrolase/DNA
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	28.56 Å
Radius of gyration Rg (electron density) rg_electron	27.38 Å
Forward intensity I(0) i0	68758400.00
Molecular weight molecular_weight	64382.0 kDa
Excluded volume excluded_volume	79899 Å³
Envelope volume envelope_volume	103500 Å³
Hydration-shell volume shell_volume	31372 Å³
Envelope diameter envelope_diameter	86.6 Å
Shell Rg shell_rg	35.00 Å
Envelope Rg envelope_rg	26.87 Å
Shape Rg shape_rg	27.39 Å
Total Rg total_rg	28.17 Å
Total atoms total_atoms	4474
Residues n_residues	550
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	85.9 Å
Rg (real space) rg_real	28.43 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	6.8760e+07
I(0) uncertainty (real space) i0_real_error	9.6030e+05
Rg (reciprocal space) rg_reciprocal	28.49 Å
I(0) (reciprocal space) i0_reciprocal	68760000.0000
Solution quality estimate total_estimate	0.9162
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	38.4 Å
Skewness Skewness skewness	0.073
Kurtosis Kurtosis kurtosis	-0.682
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12110000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.980; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.968

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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	DNA repair protein RAD2
Molecular weight formula_weight	43017.0 kDa
EC 编号 ec_number	3.1.-.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4556

SMGVHSFWDIAGPTARPVRLESLEDKRMAVDASIWIYQFLKAVRDQEGNAVKNSHITGFFRRICKLLYFGIRPVFVFDGGVPVLKRETIRQRKERRQGKRESAKSTARKLLANTTLSTSAERNVAENAFVEDELFEQQMKDKRDSDEVTMDMIKEVQELLSRFGIPYITAPMEAEAQCAELLQLNLVDGIITDDSDVFLFGGTKIYKNMFHEKNYVEFYDAESILKLLGLDRKNMIELAQLLGSDYTNGLKGMGPVSSIEVIAEFGNLKNFKDWYNNGQFDKRKQETENKFEKDLRKKLVNNEIILDDDFPSVMVYDAYMRPEVDHDTTPFVWGVPDLDMLRSFMKTQLGWPHEKSDEILIPLIRDV

来源 Source

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

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(CPTPGPAPGPTPCPAPGPAPGPCPAPAP*A)-3') ;
Molecular weight formula_weight	4627.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

CTGAGTCAGAGCAAA

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	79

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8. Citations (1)

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Unit-cell length a length_a	94.085 Å
Unit-cell length b length_b	94.085 Å
Unit-cell length c length_c	155.264 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	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.750 Å
Low-resolution limit resolution_low	39.406 Å
R factor r_factor	0.2485
R_work r_work	0.2453
R_free r_free	0.3102

fit	/app/data/saxs_computation/q0/4q0r/4q0r.fit
pddf	/app/data/pr_computation/q0/4q0r/4q0r.pr.out
profile	/app/data/saxs_computation/q0/4q0r/4q0r.dat

The catalytic core of Rad2 (complex I)

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

DNA repair protein RAD2

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)