[English] 日本語
Yorodumi
- PDB-3p4y: Helicase domain of reverse gyrase from Thermotoga maritima - P2 form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3p4y
TitleHelicase domain of reverse gyrase from Thermotoga maritima - P2 form
Componentsreverse gyrase helicase domain
KeywordsISOMERASE / TOPOISOMERASE / DNA SUPERCOILING / ARCHAEA / HELICASE
Function / homology
Function and homology information


Isomerases; Isomerases altering macromolecular conformation; Enzymes altering nucleic acid conformation / reverse gyrase activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA unwinding involved in DNA replication / DNA topological change / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
Reverse gyrase, zinc finger / Reverse gyrase zinc finger / Reverse gyrase / Reverse gyrase, TOPRIM domain / Zinc finger reverse gyrase N-terminal-type profile. / Zinc finger reverse gyrase C-terminal-type profile. / Topoisomerase (Topo) IA-type catalytic domain profile. / DNA topoisomerase, type IA, domain 2 / DNA topoisomerase, type IA, DNA-binding domain / DNA topoisomerase, type IA, central ...Reverse gyrase, zinc finger / Reverse gyrase zinc finger / Reverse gyrase / Reverse gyrase, TOPRIM domain / Zinc finger reverse gyrase N-terminal-type profile. / Zinc finger reverse gyrase C-terminal-type profile. / Topoisomerase (Topo) IA-type catalytic domain profile. / DNA topoisomerase, type IA, domain 2 / DNA topoisomerase, type IA, DNA-binding domain / DNA topoisomerase, type IA, central / DNA topoisomerase, type IA, central region, subdomain 1 / DNA topoisomerase, type IA, central region, subdomain 3 / DNA topoisomerase, type IA, core domain / DNA topoisomerase / Bacterial DNA topoisomeraes I ATP-binding domain / Bacterial DNA topoisomerase I DNA-binding domain / TOPRIM / Toprim domain / Toprim domain profile. / TOPRIM domain / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesthermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsRudolph, M.G. / Klostermeier, D.
CitationJournal: Biochemistry / Year: 2011
Title: The Conformational Flexibility of the Helicase-like Domain from Thermotoga maritima Reverse Gyrase Is Restricted by the Topoisomerase Domain.
Authors: Del Toro Duany, Y. / Klostermeier, D. / Rudolph, M.G.
History
DepositionOct 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: 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: reverse gyrase helicase domain


Theoretical massNumber of molelcules
Total (without water)48,2331
Polymers48,2331
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)61.853, 59.185, 67.650
Angle α, β, γ (deg.)90.00, 98.22, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-160-

LYS

-
Components

#1: Protein reverse gyrase helicase domain


Mass: 48232.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) thermotoga maritima (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O51934*PLUS

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.59 %

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.984 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 3.2→48.8 Å / Num. obs: 7475 / % possible obs: 91.4 % / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.171 / Rsym value: 0.171 / Net I/σ(I): 7.2
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.612 / Rsym value: 0.612 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDS(VERSION May 10data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3OIY
Resolution: 3.2→44.344 Å / SU ML: 0.49 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.297 315 4.56 %random
Rwork0.2863 ---
obs0.2868 6907 84.56 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.229 Å2 / ksol: 0.308 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--21.8067 Å20 Å20.8519 Å2
2--28.5681 Å2-0 Å2
3----27.2298 Å2
Refinement stepCycle: LAST / Resolution: 3.2→44.344 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3328 0 0 0 3328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033396
X-RAY DIFFRACTIONf_angle_d0.5434551
X-RAY DIFFRACTIONf_dihedral_angle_d12.7281287
X-RAY DIFFRACTIONf_chiral_restr0.038499
X-RAY DIFFRACTIONf_plane_restr0.002573
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.30.34771440.32963069X-RAY DIFFRACTION79
4.0313-44.34840.27381710.26613523X-RAY DIFFRACTION90
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
16.64830.55891.90133.0407-1.09915.4084-0.0680.44650.0738-0.35990.0437-0.4932-0.16861.51220.1574-0.1136-0.13710.11740.2243-0.02980.095440.418727.801419.7032
22.1098-0.8878-0.47462.6034-1.21793.90580.128-0.0133-0.7062-0.84050.06430.62931.5784-0.2334-0.1310.7089-0.0434-0.1921-0.06010.0820.555340.65272.108351.6248
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 55:279)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 280:534)

+
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://pdbjlvh1.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