[English] 日本語
Yorodumi
- PDB-2brf: Crystal Structure of the FHA Domain of Human Polynucleotide Kinas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2brf
TitleCrystal Structure of the FHA Domain of Human Polynucleotide Kinase 3' Phosphatase
ComponentsBIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE
KeywordsHYDROLASE/TRANSFERASE / FHA / FORKHEAD-ASSOCIATED / PNKP / PNK / POLYNUCLEOTIDE KINASE 3' PHOSPHATASE / DNA REPAIR / BER / SSBR / DSBR / XRCC1 / XRCC4 HYDROLASE / TRANSFERASE / BIFUNCTIONAL / HYDROLASE-TRANSFERASE complex
Function / homology
Function and homology information


purine nucleotide binding / polynucleotide 3'-phosphatase / polynucleotide 3'-phosphatase activity / polynucleotide 5'-hydroxyl-kinase / ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity / positive regulation of double-strand break repair via nonhomologous end joining / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / positive regulation of telomere maintenance / base-excision repair, gap-filling / nucleotide-excision repair ...purine nucleotide binding / polynucleotide 3'-phosphatase / polynucleotide 3'-phosphatase activity / polynucleotide 5'-hydroxyl-kinase / ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity / positive regulation of double-strand break repair via nonhomologous end joining / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / positive regulation of telomere maintenance / base-excision repair, gap-filling / nucleotide-excision repair / response to radiation / double-strand break repair via nonhomologous end joining / DNA-templated DNA replication / site of double-strand break / double-stranded DNA binding / endonuclease activity / response to oxidative stress / damaged DNA binding / DNA repair / nucleolus / nucleoplasm / ATP binding / nucleus / membrane
Similarity search - Function
Bifunctional polynucleotide phosphatase/kinase PNKP / Polynucleotide 3'-phosphatase / Polynucleotide kinase 3 phosphatase / Polynucleotide kinase 3 phosphatase / PNK, FHA domain / FHA domain / HAD-superfamily hydrolase,subfamily IIIA / AAA domain / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 ...Bifunctional polynucleotide phosphatase/kinase PNKP / Polynucleotide 3'-phosphatase / Polynucleotide kinase 3 phosphatase / Polynucleotide kinase 3 phosphatase / PNK, FHA domain / FHA domain / HAD-superfamily hydrolase,subfamily IIIA / AAA domain / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / SMAD/FHA domain superfamily / HAD superfamily / HAD-like superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Bifunctional polynucleotide phosphatase/kinase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsOliver, A.W. / Ali, A.A.E. / Pearl, L.H.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: Specific Recognition of a Multiply Phosphorylated Motif in the DNA Repair Scaffold Xrcc1 by the Fha Domain of Human Pnk.
Authors: Ali, A.A.E. / Jukes, R.M. / Pearl, L.H. / Oliver, A.W.
History
DepositionMay 4, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0013
Polymers11,8091
Non-polymers1922
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)31.812, 40.047, 37.512
Angle α, β, γ (deg.)90.00, 90.96, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE / FHA DOMAIN OF POLYNUCLEOTIDE KINASE 3' PHOSPHATASE / DNA 5'-KINASE/3'-PHOSPHATASE / POLYNUCLEOTIDE ...FHA DOMAIN OF POLYNUCLEOTIDE KINASE 3' PHOSPHATASE / DNA 5'-KINASE/3'-PHOSPHATASE / POLYNUCLEOTIDE 5'-HYDROXYL-KINASE / POLYNUCLEOTIDE 3'-PHOSPHATASE


Mass: 11809.350 Da / Num. of mol.: 1 / Fragment: FHA DOMAIN, RESIDUES 1-110
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: MODIFIED PET-17B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA2 (DE3) PLYSS
References: UniProt: Q96T60, polynucleotide 3'-phosphatase, polynucleotide 5'-hydroxyl-kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 37.6 %
Crystal growDetails: PROTEIN WAS CRYSTALLISED IN 0.1 M TRIS-HCL PH 8.5, 2.0 M AMMONIUM SULPHATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.4→37.5 Å / Num. obs: 16490 / % possible obs: 97.2 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 8.9
Reflection shellResolution: 1.4→1.44 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 3.9 / % possible all: 88

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UJX

1ujx


Resolution: 1.4→37.5 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 0.811 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.183 834 5.1 %RANDOM
Rwork0.15 ---
obs0.152 15643 88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20.02 Å2
2--0.06 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.4→37.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms755 0 10 143 908
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.022792
X-RAY DIFFRACTIONr_bond_other_d0.0020.02751
X-RAY DIFFRACTIONr_angle_refined_deg2.5122.0211087
X-RAY DIFFRACTIONr_angle_other_deg1.06831746
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.855103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.93223.44829
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.40315126
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.591157
X-RAY DIFFRACTIONr_chiral_restr0.1870.2128
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02864
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02141
X-RAY DIFFRACTIONr_nbd_refined0.2450.2120
X-RAY DIFFRACTIONr_nbd_other0.2070.2728
X-RAY DIFFRACTIONr_nbtor_refined0.1660.2387
X-RAY DIFFRACTIONr_nbtor_other0.0890.2514
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.4450.284
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2890.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3240.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2890.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1041.5639
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.232824
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.6713317
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.684.5261
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.247 21
Rwork0.185 595

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more