SAXSdb — 6tux

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

DNA repair protein complementing XP-G cells,DNA repair protein complementing XP-G cells

Homo sapiens

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 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain A； UniProt 1–112 Chain A； UniProt 750–986	Not recorded	;DNA (5'-D(PGPCPAPGPAPGPTPT)-3') ; × 1 ;DNA (5'-D(PAPAPCPTPCPTPGPC)-3') ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；295 K；5% PEG 3350, 50 mM Na Citrate pH 4.0	Resolution 3.10 Å R-free 0.303
2	Protein–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain B； UniProt 1–112 Chain B； UniProt 750–986	Not recorded	;DNA (5'-D(PGPCPAPGPAPGPTPT)-3') ; × 1 ;DNA (5'-D(PAPAPCPTPCPTPGPC)-3') ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；295 K；5% PEG 3350, 50 mM Na Citrate pH 4.0	Resolution 3.10 Å R-free 0.303

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 6TUX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5EKF Crystallization and X-ray Diffraction Data Collection of Importin-alpha from Mus musculus Complexed with a XPG NLS Peptide, fragment 1 Deposited 2015-11-03	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1054–1077（24 aa） Fragment：UNP residues 1054-1077 Chain C 1054–1077（24 aa） Fragment：UNP residues 1054-1077	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.6-0.7 M sodium citrate, 10 mM DTT	Resolution 2.00 Å R-free 0.192
6TUR human XPG, Apo1 form Deposited 2020-01-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 2–112（111 aa） Chain AAA 750–990（241 aa）	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；295 K；25% PEG 3350, 100 mM Citric acid pH 3.5	Resolution 2.90 Å R-free 0.281
6TUR human XPG, Apo1 form Deposited 2020-01-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain BBB 2–112（111 aa） Chain BBB 750–990（241 aa）	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；295 K；25% PEG 3350, 100 mM Citric acid pH 3.5	Resolution 2.90 Å R-free 0.281
6TUR human XPG, Apo1 form Deposited 2020-01-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain CCC 2–112（111 aa） Chain CCC 750–990（241 aa）	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；295 K；25% PEG 3350, 100 mM Citric acid pH 3.5	Resolution 2.90 Å R-free 0.281
6TUR human XPG, Apo1 form Deposited 2020-01-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain DDD 2–112（111 aa） Chain DDD 750–990（241 aa）	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；295 K；25% PEG 3350, 100 mM Citric acid pH 3.5	Resolution 2.90 Å R-free 0.281
6TUS human XPG, Apo2 form Deposited 2020-01-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–112（112 aa） Chain A 750–990（241 aa）	Not recorded	SO4 SULFATE ION × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；25% PEG 3350, 100 mM Bis-Tris pH 6.5, 200 mM Amm. Sulfate.	Resolution 2.50 Å R-free 0.237
6TUS human XPG, Apo2 form Deposited 2020-01-08	Different construct 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 1–112（112 aa） Chain B 750–990（241 aa）	Not recorded	SO4 SULFATE ION × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；25% PEG 3350, 100 mM Bis-Tris pH 6.5, 200 mM Amm. Sulfate.	Resolution 2.50 Å R-free 0.237
6TUW human XPG-DNA, Complex 1 Deposited 2020-01-08	Different construct Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–112（112 aa） Chain A 750–990（241 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；5% PEG 3350, 50 mM Na Citrate pH 4.0	Resolution 3.50 Å R-free 0.293
6VBH Human XPG endonuclease catalytic domain Deposited 2019-12-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–85（84 aa） Chain A 766–987（222 aa）	Not recorded	SO4 SULFATE ION × 15	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；288 K；Mixed 1:1 with 40% AmSO4, 200 mM Imidizole/Malate Buffer pH 4.2,100 mM MgCl2 X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；288 K；Mixed 1:1 wit 24% AmSO4, 200 mM Imidizole/Malate Buffer pH 4.2, 250 mM MgCl2, 0.5 mM SmSO4, 10 mM DTT X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；288 K；Mixed 1:1 with 32% AmSO4, 10 mM DTT, 200 mM Imidizole/Malate Buffer pH 4.2, and 50 mM MgCl2	Resolution 2.00 Å R-free 0.244
6VBH Human XPG endonuclease catalytic domain Deposited 2019-12-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–85（84 aa） Chain A 766–987（222 aa）	Not recorded	SO4 SULFATE ION × 30	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；288 K；Mixed 1:1 with 40% AmSO4, 200 mM Imidizole/Malate Buffer pH 4.2,100 mM MgCl2 X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；288 K；Mixed 1:1 wit 24% AmSO4, 200 mM Imidizole/Malate Buffer pH 4.2, 250 mM MgCl2, 0.5 mM SmSO4, 10 mM DTT X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；288 K；Mixed 1:1 with 32% AmSO4, 10 mM DTT, 200 mM Imidizole/Malate Buffer pH 4.2, and 50 mM MgCl2	Resolution 2.00 Å R-free 0.244
9PD3 NER dual incision complex - DuIS Deposited 2025-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric	Chain S 1–1186（1186 aa）	Mutation：D812N	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9PD4 NER dual incision complex - DuIM Deposited 2025-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric	Chain S 1–1186（1186 aa）	Mutation：D812N	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
9PD5 NER dual incision complex - NoF Deposited 2025-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric	Chain S 1–1186（1186 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.70 Å

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

View Construct and Data Evidence

UniProt name	ERCC5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–112； UniProt 1–112 Author chain A； PDBConstruct 115–351； UniProt 750–986 Author chain B； PDBConstruct 1–112； UniProt 1–112 Author chain B； PDBConstruct 115–351； UniProt 750–986

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	6tux
Deposition date deposition_date	2020-01-08
Structure title title	human XPG-DNA, Complex 2
Keywords keywords	XPG nuclease domain bound to DNA, DNA BINDING PROTEIN; DNA BINDING PROTEIN
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	34.74 Å
Radius of gyration Rg (electron density) rg_electron	34.30 Å
Forward intensity I(0) i0	119582000.00
Molecular weight molecular_weight	83518.0 kDa
Excluded volume excluded_volume	103070 Å³
Envelope volume envelope_volume	144840 Å³
Hydration-shell volume shell_volume	36971 Å³
Envelope diameter envelope_diameter	128.7 Å
Shell Rg shell_rg	38.43 Å
Envelope Rg envelope_rg	34.18 Å
Shape Rg shape_rg	34.29 Å
Total Rg total_rg	34.65 Å
Total atoms total_atoms	5860
Residues n_residues	675
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	120.7 Å
Rg (real space) rg_real	34.89 Å
Rg uncertainty (real space) rg_real_error	1.04 Å
I(0) (real space) i0_real	1.1960e+08
I(0) uncertainty (real space) i0_real_error	2.1410e+06
Rg (reciprocal space) rg_reciprocal	34.80 Å
I(0) (reciprocal space) i0_reciprocal	119600000.0000
Solution quality estimate total_estimate	0.8662
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	36.8 Å
Skewness Skewness skewness	0.461
Kurtosis Kurtosis kurtosis	-0.207
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	18340000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.818; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.945; Smooth: 0.857

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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 complementing XP-G cells,DNA repair protein complementing XP-G cells
Molecular weight formula_weight	40304.4 kDa
EC 编号 ec_number	3.1.-.-,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	5860

MGVQGLWKLLECSGRQVSPEALEGKILAVDISIWLNQALKGVRDRHGNSIENPHLLTLFHRLCKLLFFRIRPIFVFDGDAPLLKKQTLVKRRQRKDLASSDSRKTTEKLLKTGTLKAQKQQQERIAATVTGQMFLESQELLRLFGIPYIQAPMEAEAQCAILDLTDQTSGTITDDSAIWLFGARHVYRNFFNKNKFVEYYQYVDFHNQLGLDRNKLINLAYLLGSDYTEGIPTVGCVTAMEILNEFPGHGLEPLLKFSEWWHEAQKNPKIRPNPHDTKVKKKLRTLQLTPGFPNPAVAEAYLKPVVDDSKGSFLWGKPDLDKIREFCQRYFGWNRTKTDESLFPVLKQLDA

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(PGPCPAPGPAPGPTPT)-3') ;
Molecular weight formula_weight	3364.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,E

TTGCAGAGTTC

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(PAPAPCPTPCPTPGPC)-3') ;
Molecular weight formula_weight	3358.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D,F

GAACTCTGCAG

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8. Citations (1)

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Unit-cell length a length_a	127.650 Å
Unit-cell length b length_b	127.650 Å
Unit-cell length c length_c	118.960 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 4 21 2
Space-group number int_tables_number	90
Crystal system crystal_system	tetragonal

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	49.670 Å
R factor r_factor	0.2487
R_work r_work	0.2470
R_free r_free	0.3027

fit	/app/data/saxs_computation/tu/6tux/6tux.fit
pddf	/app/data/pr_computation/tu/6tux/6tux.pr.out
profile	/app/data/saxs_computation/tu/6tux/6tux.dat

human XPG-DNA, Complex 2

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

DNA repair protein complementing XP-G cells,DNA repair protein complementing XP-G cells

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 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)