[English] 日本語
Yorodumi
- PDB-3hr8: Crystal Structure of Thermotoga maritima RecA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hr8
TitleCrystal Structure of Thermotoga maritima RecA
ComponentsProtein recA
KeywordsRECOMBINATION / Alpha and beta proteins (a/b / a+b) / ATP-binding / Cytoplasm / DNA damage / DNA recombination / DNA repair / DNA-binding / Nucleotide-binding / SOS response
Function / homology
Function and homology information


SOS response / ATP-dependent activity, acting on DNA / single-stranded DNA binding / DNA recombination / damaged DNA binding / DNA repair / ATP binding / cytoplasm
Similarity search - Function
RecA protein, C-terminal domain / Rec A Protein; domain 2 / DNA recombination/repair protein RecA, conserved site / DNA recombination and repair protein RecA, C-terminal / recA signature. / DNA recombination and repair protein RecA / recA bacterial DNA recombination protein / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain ...RecA protein, C-terminal domain / Rec A Protein; domain 2 / DNA recombination/repair protein RecA, conserved site / DNA recombination and repair protein RecA, C-terminal / recA signature. / DNA recombination and repair protein RecA / recA bacterial DNA recombination protein / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / 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 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLee, S. / Kim, T.G. / Jeong, E.-Y. / Ban, C. / Jeon, W.-J. / Min, K.I. / Song, K.-M. / Heo, S.-D. / Ku, J.K.
CitationJournal: to be published
Title: Crystal Structure of RecA Protein from Thermotoga maritima MSB8
Authors: Lee, S. / Kim, T.G. / Ku, J.K. / Ban, C.
History
DepositionJun 9, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 1, 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: Protein recA


Theoretical massNumber of molelcules
Total (without water)38,8481
Polymers38,8481
Non-polymers00
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.137, 102.137, 81.512
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein Protein recA / DNA Recombinase A / Recombinase A


Mass: 38847.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: Thermotoga maritima MSB8 / Gene: recA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P36203
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 3.16 Å3/Da / Density % sol: 61.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M Sodium Acetate trihydrate (pH 4.6), 8% (w/v) PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 13, 2009 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. all: 48111 / Num. obs: 45897 / % possible obs: 95.4 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.076 / Rsym value: 0.052
Reflection shellResolution: 1.73→1.79 Å / Redundancy: 2.4 % / Num. unique all: 3251 / % possible all: 64.9

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OFO

2ofo


Resolution: 1.95→23.492 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.875 / SU ML: 0.14 / σ(F): 1.56 / Phase error: 20.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.23 1801 5.13 %
Rwork0.195 33335 -
obs0.197 35136 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.801 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso max: 127.51 Å2 / Biso mean: 43.843 Å2 / Biso min: 17.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å2-0 Å20 Å2
2--0.29 Å2-0 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.95→23.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2619 0 0 299 2918
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092653
X-RAY DIFFRACTIONf_angle_d1.2913571
X-RAY DIFFRACTIONf_chiral_restr0.09410
X-RAY DIFFRACTIONf_plane_restr0.004462
X-RAY DIFFRACTIONf_dihedral_angle_d18.9141004
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-2.0030.2941410.2422535267699
2.003-2.0620.2371350.2312526266199
2.062-2.1280.2761250.2062570269599
2.128-2.2040.211330.2032544267799
2.204-2.2920.2331380.1852572271099
2.292-2.3970.2421520.19825302682100
2.397-2.5230.2351440.19225442688100
2.523-2.6810.2541180.18925882706100
2.681-2.8870.2421340.19425642698100
2.887-3.1770.2121530.19925742727100
3.177-3.6350.2091380.18725832721100
3.635-4.5750.181430.1725802723100
4.575-23.4930.2591470.226252772100

+
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