SAXSdb — 2brf

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

BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–110	Fragment：FHA DOMAIN, RESIDUES 1-110	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：PROTEIN WAS CRYSTALLISED IN 0.1 M TRIS-HCL PH 8.5, 2.0 M AMMONIUM SULPHATE	Resolution 1.40 Å R-free 0.183

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 2BRF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2W3O Crystal structure of the human PNKP FHA domain in complex with an XRCC1-derived phosphopeptide Deposited 2008-11-13	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–110（110 aa） Fragment：FHA DOMAIN, RESIDUES 1-110	Mutation：YES	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.1 M TRIS-HCL PH 8.5, 0.25 M CACL2, 28% W/V PEG 4000, 0.2 M NDSB-221	Resolution 1.85 Å R-free 0.236
2W3O Crystal structure of the human PNKP FHA domain in complex with an XRCC1-derived phosphopeptide Deposited 2008-11-13	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–110（110 aa） Fragment：FHA DOMAIN, RESIDUES 1-110	Mutation：YES	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.1 M TRIS-HCL PH 8.5, 0.25 M CACL2, 28% W/V PEG 4000, 0.2 M NDSB-221	Resolution 1.85 Å R-free 0.236

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PNKP_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–110； UniProt 1–110

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	2brf
Deposition date deposition_date	2005-05-04
Structure title title	Crystal Structure of the FHA Domain of Human Polynucleotide Kinase 3' Phosphatase
Keywords keywords	;HYDROLASE/TRANSFERASE, FHA, FORKHEAD-ASSOCIATED, PNKP, PNK, POLYNUCLEOTIDE KINASE 3' PHOSPHATASE, DNA REPAIR, BER, SSBR, DSBR, XRCC1, XRCC4 HYDROLASE, TRANSFERASE, BIFUNCTIONAL, HYDROLASE-TRANSFERASE complex ;; HYDROLASE/TRANSFERASE
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	14.35 Å
Radius of gyration Rg (electron density) rg_electron	12.77 Å
Forward intensity I(0) i0	2580750.00
Molecular weight molecular_weight	10898.0 kDa
Excluded volume excluded_volume	13573 Å³
Envelope volume envelope_volume	15064 Å³
Hydration-shell volume shell_volume	10247 Å³
Envelope diameter envelope_diameter	46.4 Å
Shell Rg shell_rg	18.27 Å
Envelope Rg envelope_rg	13.14 Å
Shape Rg shape_rg	12.74 Å
Total Rg total_rg	14.10 Å
Total atoms total_atoms	765
Residues n_residues	100
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	48.1 Å
Rg (real space) rg_real	14.28 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	2.5810e+06
I(0) uncertainty (real space) i0_real_error	2.8150e+04
Rg (reciprocal space) rg_reciprocal	14.29 Å
I(0) (reciprocal space) i0_reciprocal	2581000.0000
Solution quality estimate total_estimate	0.8801
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.9 Å
Skewness Skewness skewness	0.192
Kurtosis Kurtosis kurtosis	-0.283
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	356900.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.817; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.991

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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	BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE
Molecular weight formula_weight	11809.4 kDa
EC 编号 ec_number	3.1.3.32, 2.7.1.78
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	928

MGEVEAPGRLWLESPPGEAPPIFLPSDGQALVLGRGPLTQVTDRKCSRTQVELVADPETRTVAVKQLGVNPSTTGTQELKPGLEGSLGVGDTLYLVNGLHPLTLRWEETR

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 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	143

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2brfa1
Class class	b — All beta proteins
Fold Fold fold	b.26 — SMAD/FHA domain
Superfamily Superfamily superfamily	b.26.1 — SMAD/FHA domain
Family Family family	b.26.1.2 — FHA domain

CATH v4.4 (1 domains)

Domain ID domain_id	2brfA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	200 — Tumour Suppressor Smad4
Homologous superfamily homologous superfamily	20 —

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8. Citations (1)

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Unit-cell length a length_a	31.812 Å
Unit-cell length b length_b	40.047 Å
Unit-cell length c length_c	37.512 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.96 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	37.500 Å
R factor r_factor	0.1520
R_work r_work	0.1500
R_free r_free	0.1830

fit	/app/data/saxs_computation/br/2brf/2brf.fit
pddf	/app/data/pr_computation/br/2brf/2brf.pr.out
profile	/app/data/saxs_computation/br/2brf/2brf.dat

Crystal Structure of the FHA Domain of Human Polynucleotide Kinase 3' Phosphatase

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

BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE

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