[English] 日本語
Yorodumi
- PDB-2p6r: Crystal structure of superfamily 2 helicase Hel308 in complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2p6r
TitleCrystal structure of superfamily 2 helicase Hel308 in complex with unwound DNA
Components
  • 25-MER
  • 5'-D(*CP*TP*AP*GP*AP*GP*AP*CP*TP*AP*TP*CP*GP*AP*T)-3'
  • afUHEL308 HELICASE
KeywordsDNA binding protein/DNA / PROTEIN-DNA COMPLEX / SF2 HELICASE / ARCHAEAL HELICASE / DNA REPAIR / DNA binding protein-DNA COMPLEX
Function / homology
Function and homology information


Sec63 N-terminal domain-like fold - #30 / Sec63 N-terminal domain-like fold / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBuettner, K. / Nehring, S. / Hopfner, K.P.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2007
Title: Structural basis for DNA duplex separation by a superfamily-2 helicase.
Authors: Buttner, K. / Nehring, S. / Hopfner, K.P.
History
DepositionMar 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE RESIDUES 1-691 MATCH THE GENBANK ACCESSION NP_071282. NO SUITABLE UNIPROT SEQUENCE ...SEQUENCE RESIDUES 1-691 MATCH THE GENBANK ACCESSION NP_071282. NO SUITABLE UNIPROT SEQUENCE DATABASE REFERENCE WAS AVAILABLE AT THE TIME OF PROCESSING THIS ENTRY

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
X: 25-MER
Y: 5'-D(*CP*TP*AP*GP*AP*GP*AP*CP*TP*AP*TP*CP*GP*AP*T)-3'
A: afUHEL308 HELICASE


Theoretical massNumber of molelcules
Total (without water)91,3743
Polymers91,3743
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.379, 138.379, 252.973
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

-
Components

#1: DNA chain 25-MER


Mass: 7657.960 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*TP*AP*GP*AP*GP*AP*CP*TP*AP*TP*CP*GP*AP*T)-3'


Mass: 4593.011 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein afUHEL308 HELICASE


Mass: 79122.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Plasmid: pET-29 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.86 Å3/Da / Density % sol: 68.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M MES pH 6.0; 22% MPD; 0.1M MgAcetate; 10% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MES11
2MPD11
3MgAcetate11
4Glycerol11
5H2O11
6MES12
7MPD12
8MgAcetate12
9Glycerol12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.92 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 54172 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.089 / Rsym value: 0.09 / Net I/σ(I): 16.93
Reflection shellHighest resolution: 3 Å / Rmerge(I) obs: 0.168 / Mean I/σ(I) obs: 8.97 / Rsym value: 0.194 / % possible all: 99.9

-
Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
XDSdata scaling
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→20 Å / σ(F): 611 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.2748 2883 9.8 %
Rwork0.2317 --
obs-54172 97.9 %
Solvent computationBsol: 25.606 Å2
Displacement parametersBiso mean: 59.128 Å2
Baniso -1Baniso -2Baniso -3
1--3.49 Å2-12.242 Å20 Å2
2---3.49 Å20 Å2
3---6.98 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5406 813 0 0 6219
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.258
X-RAY DIFFRACTIONc_mcbond_it1.4251.5
X-RAY DIFFRACTIONc_scbond_it1.9482
X-RAY DIFFRACTIONc_mcangle_it2.4632
X-RAY DIFFRACTIONc_scangle_it3.092.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION3CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top

+
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