[English] 日本語
Yorodumi
- PDB-2rhf: D. radiodurans RecQ HRDC domain 3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2rhf
TitleD. radiodurans RecQ HRDC domain 3
ComponentsDNA helicase RecQ
KeywordsHYDROLASE / HRDC / RecQ / helicase / D. radiodurans / ATP-binding / Nucleotide-binding
Function / homology
Function and homology information


bacterial nucleoid / four-way junction helicase activity / replisome / SOS response / DNA 3'-5' helicase / DNA duplex unwinding / 3'-5' DNA helicase activity / isomerase activity / chromosome / DNA recombination ...bacterial nucleoid / four-way junction helicase activity / replisome / SOS response / DNA 3'-5' helicase / DNA duplex unwinding / 3'-5' DNA helicase activity / isomerase activity / chromosome / DNA recombination / DNA replication / hydrolase activity / DNA repair / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
DNA helicase, ATP-dependent, RecQ type, bacterial / HRDC domain / RQC domain / RQC / RQC domain / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / Helicase and RNase D C-terminal / HRDC domain ...DNA helicase, ATP-dependent, RecQ type, bacterial / HRDC domain / RQC domain / RQC / RQC domain / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / Helicase and RNase D C-terminal / HRDC domain / HRDC domain / HRDC domain profile. / HRDC domain superfamily / HRDC-like superfamily / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / DNA polymerase; domain 1 / helicase superfamily c-terminal 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, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / DNA helicase RecQ
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.1 Å
AuthorsKeck, J.L. / Killoran, M.P.
CitationJournal: Nucleic Acids Res. / Year: 2008
Title: Structure and function of the regulatory C-terminal HRDC domain from Deinococcus radiodurans RecQ.
Authors: Killoran, M.P. / Keck, J.L.
History
DepositionOct 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA helicase RecQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5812
Polymers8,4861
Non-polymers951
Water3,081171
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.978, 49.978, 83.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-946-

HOH

DetailsAthours state that the biological molecule is unknown.

-
Components

#1: Protein DNA helicase RecQ


Mass: 8486.380 Da / Num. of mol.: 1 / Fragment: D. radiodurans HRDC domain 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: R1 / Gene: recQ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9RUU2
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 3.08 Å3/Da / Density % sol: 60.01 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 1.8 M Na-K Phosphate pH 4.0, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9999, 0.9797
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 26, 2005
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.99991
20.97971
ReflectionResolution: 1.1→83.6 Å / Num. all: 42318 / Num. obs: 40879 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.067
Reflection shellResolution: 1.1→1.16 Å / Mean I/σ(I) obs: 1.8 / Rsym value: 0.419 / % possible all: 78.7

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 1.1→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 0.76 / SU ML: 0.017 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.031 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19399 2061 5 %RANDOM
Rwork0.17715 ---
obs0.17798 38922 96.93 %-
all-42294 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.709 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2--0.28 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms588 0 5 171 764
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022605
X-RAY DIFFRACTIONr_angle_refined_deg1.2261.988818
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.427575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.87323.33330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.73215106
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.587157
X-RAY DIFFRACTIONr_chiral_restr0.0950.295
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02453
X-RAY DIFFRACTIONr_nbd_refined0.2260.2323
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2431
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2112
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3880.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0890.235
X-RAY DIFFRACTIONr_mcbond_it1.2531.5387
X-RAY DIFFRACTIONr_mcangle_it1.7742600
X-RAY DIFFRACTIONr_scbond_it2.4443236
X-RAY DIFFRACTIONr_scangle_it3.4064.5218
X-RAY DIFFRACTIONr_rigid_bond_restr1.423623
X-RAY DIFFRACTIONr_sphericity_free3.6193171
X-RAY DIFFRACTIONr_sphericity_bonded3.8013599
LS refinement shellResolution: 1.1→1.128 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.441 66 -
Rwork0.319 1638 -
obs--75.63 %

+
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