[English] 日本語
Yorodumi
- PDB-3u7f: Crystal structure of mPNKP catalytic fragment (D170A) bound to si... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3u7f
TitleCrystal structure of mPNKP catalytic fragment (D170A) bound to single-stranded DNA (TCCTCp)
Components
  • Bifunctional polynucleotide phosphatase/kinase
  • DNA
KeywordsHYDROLASE / TRANSFERASE/DNA / protein-DNA complex / HAD family / pnkp / DNA repair / phosphatase / TRANSFERASE-DNA complex
Function / homology
Function and homology information


polynucleotide 3'-phosphatase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase activity / ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / DNA ligation involved in DNA repair / SCF ubiquitin ligase complex / positive regulation of double-strand break repair via nonhomologous end joining / protein K63-linked ubiquitination / positive regulation of telomere capping ...polynucleotide 3'-phosphatase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase activity / ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / DNA ligation involved in DNA repair / SCF ubiquitin ligase complex / positive regulation of double-strand break repair via nonhomologous end joining / protein K63-linked ubiquitination / positive regulation of telomere capping / ubiquitin-like ligase-substrate adaptor activity / positive regulation of telomere maintenance via telomerase / double-strand break repair via nonhomologous end joining / site of double-strand break / double-stranded DNA binding / response to oxidative stress / phosphorylation / DNA repair / DNA damage response / nucleolus / nucleoplasm / ATP binding / nucleus
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 / SMAD/FHA domain superfamily / HAD superfamily/HAD-like ...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 / SMAD/FHA domain superfamily / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / DNA / Bifunctional polynucleotide phosphatase/kinase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsCoquelle, N. / Havali, Z. / Bernstein, N. / Green, R. / Glover, J.N.M.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural basis for the phosphatase activity of polynucleotide kinase/phosphatase on single- and double-stranded DNA substrates.
Authors: Coquelle, N. / Havali-Shahriari, Z. / Bernstein, N. / Green, R. / Glover, J.N.
#1: Journal: Mol.Cell / Year: 2005
Title: The molecular architecture of the mammalian DNA repair enzyme, polynucleotide kinase.
Authors: Bernstein, N.K. / Williams, R.S. / Rakovszky, M.L. / Cui, D. / Green, R. / Karimi-Busheri, F. / Mani, R.S. / Galicia, S. / Koch, C.A. / Cass, C.E. / Durocher, D. / Weinfeld, M. / Glover, J.N.
History
DepositionOct 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Bifunctional polynucleotide phosphatase/kinase
X: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3929
Polymers43,8102
Non-polymers5837
Water7,368409
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-25 kcal/mol
Surface area18040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.600, 62.330, 67.970
Angle α, β, γ (deg.)90.000, 91.810, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein / DNA chain , 2 types, 2 molecules BX

#1: Protein Bifunctional polynucleotide phosphatase/kinase / DNA 5'-kinase/3'-phosphatase / Polynucleotide kinase-3'-phosphatase / Polynucleotide 3'-phosphatase ...DNA 5'-kinase/3'-phosphatase / Polynucleotide kinase-3'-phosphatase / Polynucleotide 3'-phosphatase / 2'(3')-polynucleotidase / Polynucleotide 5'-hydroxyl-kinase


Mass: 42378.699 Da / Num. of mol.: 1 / Mutation: D170A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pnkp / Plasmid: pet19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9JLV6, polynucleotide 3'-phosphatase, polynucleotide 5'-hydroxyl-kinase
#2: DNA chain DNA /


Mass: 1430.974 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA substrate of PNKP phosphatase domain

-
Non-polymers , 4 types, 416 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 2.06 Å3/Da / Density % sol: 40.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% PEG 3350, pH 7, vapor diffusion, hanging drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 12, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.8→46 Å / Num. all: 33004 / Num. obs: 33004 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.887 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 9.27
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.8-1.850.622.6394442578199.5
1.85-1.90.5283.2686462301199.9
1.9-1.950.4464.09791721091100
1.95-20.4014.8571511898199.9
2-2.10.3165.731228332551100
2.1-2.20.2726.64102432704199.9
2.2-30.1529.84152210948199.9
3-50.06317.58210485623199.7
5-100.06119.4949511381198.8
10-460.05520.4645207198.1

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
MxDCdata collection
XDSdata reduction
PHASERphasing
RefinementResolution: 1.8→45.928 Å / Occupancy max: 1 / Occupancy min: 0.32 / SU ML: 0.41 / σ(F): -3 / Phase error: 19.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2143 1649 5 %
Rwork0.1687 --
obs0.171 33002 99.77 %
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.371 Å2 / ksol: 0.408 e/Å3
Displacement parametersBiso max: 60.65 Å2 / Biso mean: 13.714 Å2 / Biso min: 0 Å2
Baniso -1Baniso -2Baniso -3
1--0.5044 Å2-0 Å2-0.9723 Å2
2---0.4091 Å2-0 Å2
3----0.8266 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2929 39 34 409 3411
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.02580.0005-0.01030.01120.00640.0289-0.027-0.0292-0.01850.018-0.0294-0.01840.03180.0115-0.1901-0.0240.02520.022-0.0287-0.0386-0.05622.1475-16.312348.7576
20.0454-0.040.01650.0654-0.01990.02390.00790.0185-0.0016-0.0189-0.0185-0.03560.01630.03-0.01760.0460.04210.0241-0.02220.0816-0.00599.3418-24.514147.3882
30.0159-0.0077-0.01110.0282-0.02760.0383-0.0277-0.01690.02740.0166-0-0.0271-0.00710.0192-0.0776-0.1016-0.09630.0071-0.11320.0254-0.01334.7981-11.170138.9089
40.0241-0.00740.00580.0454-0.00180.10410.0039-0.00640.03950.0066-0.0009-0.0585-0.05980.0254-0.0320.0363-0.02460.0067-0.0382-0.03060.04367.5256-0.202642.102
50.0650.07360.04020.1394-0.04710.19660.00230.00160.01240.01930.0020.0372-0.0317-0.0739-0.023-0.0010.05570.02250.04610.0012-0.001620.6106-8.18255.8845
60.22580.14410.10460.2277-0.0090.3412-0.00570.0689-0.0544-0.0774-0.0014-0.05680.08910.1372-0.00580.04780.02850.00480.0476-0.0068-0.011630.1872-14.79437.3278
70.0094-0.0119-0.00930.01470.01190.00920.007-0.0249-0.02660.041-0.0097-0.02780.00360.0304-0.00610.0640.0314-0.0440.1606-0.03090.073926.5302-15.423823.148
80.15850.0480.01050.16750.01830.0319-0.01660.05230.0321-0.07860.0315-0.0013-0.01770.00440.0120.0057-0.015-0.02860.02580.02060.010418.4788-6.928814.1216
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain B and (resseq 142:217)B142 - 217
2X-RAY DIFFRACTION2chain B and (resseq 218:242)B218 - 242
3X-RAY DIFFRACTION3chain B and (resseq 243:316)B243 - 316
4X-RAY DIFFRACTION4chain B and (resseq 317:341)B317 - 341
5X-RAY DIFFRACTION5chain B and (resseq 342:384)B342 - 384
6X-RAY DIFFRACTION6chain B and (resseq 385:466)B385 - 466
7X-RAY DIFFRACTION7chain B and (resseq 467:484)B467 - 484
8X-RAY DIFFRACTION8chain B and (resseq 485:522)B485 - 522

+
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