[English] 日本語
Yorodumi
- PDB-6fk4: Structure of 3' phosphatase NExo (WT) from Neisseria bound to DNA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fk4
TitleStructure of 3' phosphatase NExo (WT) from Neisseria bound to DNA substrate
Components
  • DNA (5'-D(P*GP*CP*TP*AP*GP*CP*GP*AP*AP*GP*CP*TP*AP*GP*A)-3')
  • Exodeoxyribonuclease III
KeywordsDNA BINDING PROTEIN / 3' phosphatase / base excision DNA repair.
Function / homology
Function and homology information


double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / endonuclease activity / DNA repair / DNA binding / metal ion binding
Similarity search - Function
Exodeoxyribonuclease III-like / AP endonuclease 1, binding site / AP endonucleases family 1 signature 1. / AP endonuclease 1 / AP endonucleases family 1 profile. / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily ...Exodeoxyribonuclease III-like / AP endonuclease 1, binding site / AP endonucleases family 1 signature 1. / AP endonuclease 1 / AP endonucleases family 1 profile. / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Exodeoxyribonuclease III
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria)
other sequences (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.297 Å
AuthorsSilhan, J. / Zhao, Q. / Boura, E. / Thomson, H. / Foster, A. / Tang, C.M. / Freemont, P.S. / Baldwin, G.S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust084369/Z/ 07/Z United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structural basis for recognition and repair of the 3'-phosphate by NExo, a base excision DNA repair nuclease from Neisseria meningitidis.
Authors: Silhan, J. / Zhao, Q. / Boura, E. / Thomson, H. / Forster, A. / Tang, C.M. / Freemont, P.S. / Baldwin, G.S.
History
DepositionJan 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Exodeoxyribonuclease III
B: DNA (5'-D(P*GP*CP*TP*AP*GP*CP*GP*AP*AP*GP*CP*TP*AP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0263
Polymers34,9082
Non-polymers1181
Water1,17165
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-17 kcal/mol
Surface area13100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.156, 59.156, 292.091
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Exodeoxyribonuclease III


Mass: 29318.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (strain MC58) (bacteria)
Strain: MC58 / Gene: xthA, NMB0399 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9K100, exodeoxyribonuclease III
#2: DNA chain DNA (5'-D(P*GP*CP*TP*AP*GP*CP*GP*AP*AP*GP*CP*TP*AP*GP*A)-3')


Mass: 5589.642 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 3' Phosphate residue at the last nucleotide / Source: (synth.) other sequences (unknown)
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 3.66 Å3/Da / Density % sol: 66.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 100 mM imidazole pH = 6.6, 55 mM (NH4)2SO4, 10% (w/v) PEG 8000, 16 - 19 % (v/v) MPD,

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.3→48.68 Å / Num. all: 153122 / Num. obs: 15625 / % possible obs: 99 % / Redundancy: 6.3 % / Biso Wilson estimate: 47.41 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07849 / Rrim(I) all: 0.08586 / Net I/σ(I): 13.79
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.582 / Mean I/σ(I) obs: 2.2 / Num. measured obs: 15384 / Num. unique all: 2274 / CC1/2: 0.95 / Rpim(I) all: 0.239 / Rrim(I) all: 0.63 / % possible all: 96.9

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JC4

2jc4


Resolution: 2.297→41.566 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.23 1199 4.98 %
Rwork0.1985 --
obs0.2001 24060 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.297→41.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2061 317 8 65 2451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032479
X-RAY DIFFRACTIONf_angle_d0.6163441
X-RAY DIFFRACTIONf_dihedral_angle_d16.581412
X-RAY DIFFRACTIONf_chiral_restr0.045376
X-RAY DIFFRACTIONf_plane_restr0.004390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2974-2.38940.37711310.29992410X-RAY DIFFRACTION96
2.3894-2.49810.31681370.27112452X-RAY DIFFRACTION99
2.4981-2.62980.29381160.23942478X-RAY DIFFRACTION98
2.6298-2.79450.26251290.23232495X-RAY DIFFRACTION99
2.7945-3.01030.26971110.22692531X-RAY DIFFRACTION99
3.0103-3.31310.23811280.22652537X-RAY DIFFRACTION99
3.3131-3.79220.2371510.19082550X-RAY DIFFRACTION100
3.7922-4.77670.18561530.16962590X-RAY DIFFRACTION100
4.7767-41.57310.2121430.1742818X-RAY DIFFRACTION100

+
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