SAXSdb — 2kn7

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

DNA repair endonuclease XPF

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 Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 842–908 Chain D； UniProt 842–908	Fragment：residues in UNP 842-908	;DNA (5'-D(CPAPGPTPGPGPCPTPGPA)-3') ; × 2	SOLUTION NMR NMR measurement conditions：pH 5.2；293.8 K；Ionic strength (raw mmCIF value) 80-100；Pressure ambient NMR sample composition：80mM sodium phosphate-1, 2mM sodium chloride-2, 0.005-0.010mM AEBSF protease inhibitor-3, 95% H2O/5% D2O \| 95% H2O/5% 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 2KN7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1Z00 Solution structure of the C-terminal domain of ERCC1 complexed with the C-terminal domain of XPF Deposited 2005-03-01	Different construct Different mutation/modification Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 823–905（83 aa） Fragment：C-TERMINAL DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；295.5 K；Ionic strength (raw mmCIF value) 50mM phosphate, 100mM NaCl；Pressure 1 NMR sample composition 1.5mM ERCC1-XPF U-15N,13C; 50mM phosphate buffer NA: 92% H2O, 8% D2O \| 92% H2O, 8% D2O NMR sample composition 1mM ERCC1-XPF U-15N; 50mM phosphate buffer NA: 92% H2O, 8% D2O \| 92% H2O, 8% D2O	Resolution not provided
2A1J Crystal Structure of the Complex between the C-Terminal Domains of Human XPF and ERCC1 Deposited 2005-06-20	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 A 837–898（62 aa） Fragment：C-terminal domain	Not recorded	HG MERCURY (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；295 K；Sodium Citrate, Ammonium Sulfate, Sodium Chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.70 Å R-free 0.275
2A1J Crystal Structure of the Complex between the C-Terminal Domains of Human XPF and ERCC1 Deposited 2005-06-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 837–898（62 aa） Fragment：C-terminal domain	Not recorded	HG MERCURY (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；295 K；Sodium Citrate, Ammonium Sulfate, Sodium Chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.70 Å R-free 0.275
2AQ0 Solution structure of the human homodimeric dna repair protein XPF Deposited 2005-08-17	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 823–905（83 aa） Fragment：residues 823-905 Chain B 823–905（83 aa） Fragment：residues 823-905	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；293.6 K；Ionic strength (raw mmCIF value) 400mM NaCl；Pressure 1 NMR sample composition 1.2MM XPF U-15N,13C; 10mM phosphate; 400mM sodium chloride; 92 % h2o, 8% d2o \| 92% H2O, 8% D2O	Resolution not provided
2MUT Solution structure of the F231L mutant ERCC1-XPF dimerization region Deposited 2014-09-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 834–916（83 aa） Fragment：UNP residues 834-916	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；290 K；Ionic strength (raw mmCIF value) 250；Pressure ambient NMR sample composition 0.4 mM [U-100% 13C; U-100% 15N] protein_1, 0.4 mM [U-100% 13C; U-100% 15N] protein_2, 8 % D2O, 50 mM sodium phosphate, 100 mM sodium chloride, 92% H2O/8% D2O \| 92% H2O/8% D2O	Resolution not provided
6SXA XPF-ERCC1 Cryo-EM Structure, Apo-form Deposited 2019-09-25	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 F 1–916（916 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8；20 mM HEPES pH 7.8, 150 mM NaCl, 1 mM TCEP, 0.01% CHAPS cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6SXB XPF-ERCC1 Cryo-EM Structure, DNA-Bound form Deposited 2019-09-25	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain F 1–916（916 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8；20 mM HEPES pH 7.8, 150 mM NaCl, 1 mM TCEP, 0.01% CHAPS cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.90 Å
9PCP NER dual incision complex - NoG Deposited 2025-06-28	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 × 13 PDB declaration: 15-meric	Chain Q 1–916（916 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 6 CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.30 Å
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 Q 1–916（916 aa）	Not recorded	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 Q 1–916（916 aa）	Not recorded	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
9QEC Cryo-EM structure of the XPF-ERCC1-XPA complex Deposited 2025-03-08	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–916（916 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9QED Cryo-EM structure of the XPF-ERCC1-SLX4(330-555)-SLX4IP complex Deposited 2025-03-09	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–916（916 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9QEE Cryo-EM structure of a DNA-bound XPF-ERCC1-SLX4(330-555)-SLX4IP complex Deposited 2025-03-09	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 × 4 PDB declaration: hexameric	Chain A 1–916（916 aa）	Not recorded	MN MANGANESE (II) ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å

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

View Construct and Data Evidence

UniProt name	XPF_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–67； UniProt 842–908 Author chain D； PDBConstruct 1–67； UniProt 842–908

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	2kn7
Deposition date deposition_date	2009-08-16
Structure title title	Structure of the XPF-single strand DNA complex
Keywords keywords	NER, XPF/ERCC1, HhH, Protein-ssDNA complex, HYDROLASE-DNA COMPLEX; HYDROLASE/DNA
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	20.23 Å
Radius of gyration Rg (electron density) rg_electron	18.65 Å
Forward intensity I(0) i0	3523740000.00
Molecular weight molecular_weight	419580.0 kDa
Excluded volume excluded_volume	489390 Å³
Envelope volume envelope_volume	50568 Å³
Hydration-shell volume shell_volume	19907 Å³
Envelope diameter envelope_diameter	85.4 Å
Shell Rg shell_rg	28.15 Å
Envelope Rg envelope_rg	23.73 Å
Shape Rg shape_rg	18.60 Å
Total Rg total_rg	18.87 Å
Total atoms total_atoms	54400
Residues n_residues	3061
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	73.6 Å
Rg (real space) rg_real	20.39 Å
Rg uncertainty (real space) rg_real_error	0.73 Å
I(0) (real space) i0_real	3.5240e+09
I(0) uncertainty (real space) i0_real_error	4.3070e+07
Rg (reciprocal space) rg_reciprocal	20.36 Å
I(0) (reciprocal space) i0_reciprocal	3524000000.0000
Solution quality estimate total_estimate	0.7378
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	18.9 Å
Skewness Skewness skewness	0.516
Kurtosis Kurtosis kurtosis	-0.238
Angular range angular_range	— – 0.3950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1036000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.638; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.677; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2kn7a_
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.2 — RuvA domain 2-like
Family Family family	a.60.2.5 — Hef domain-like

Domain ID domain_id	d2kn7d_
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.2 — RuvA domain 2-like
Family Family family	a.60.2.5 — Hef domain-like

CATH v4.4 (2 domains)

Domain ID domain_id	2kn7A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

Domain ID domain_id	2kn7D00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

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8. Citations (1)

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Description description	DNA repair endonuclease XPF
Molecular weight formula_weight	7423.4 kDa
EC 编号 ec_number	3.1.-.-
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	54400

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

Description description	;DNA (5'-D(CPAPGPTPGPGPCPTPGPA)-3') ;
Molecular weight formula_weight	3085.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B,C

Structure of the XPF-single strand DNA complex

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

DNA repair endonuclease XPF

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/kn/2kn7/2kn7.fit
pddf	/app/data/pr_computation/kn/2kn7/2kn7.pr.out
profile	/app/data/saxs_computation/kn/2kn7/2kn7.dat