[English] 日本語
Yorodumi
- PDB-2h5x: RuvA from Mycobacterium tuberculosis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2h5x
TitleRuvA from Mycobacterium tuberculosis
ComponentsHolliday junction ATP-dependent DNA helicase ruvA
KeywordsDNA BINDING PROTEIN / RECOMBINATION / RUVA / HOLLIDAY JUNCTION BINDING
Function / homology
Function and homology information


Holliday junction helicase complex / Holliday junction resolvase complex / four-way junction helicase activity / SOS response / four-way junction DNA binding / double-strand break repair via homologous recombination / DNA recombination / DNA helicase / DNA repair / DNA damage response ...Holliday junction helicase complex / Holliday junction resolvase complex / four-way junction helicase activity / SOS response / four-way junction DNA binding / double-strand break repair via homologous recombination / DNA recombination / DNA helicase / DNA repair / DNA damage response / ATP hydrolysis activity / DNA binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Holliday junction DNA helicase RuvA, C-terminal / DNA helicase, Holliday junction RuvA type, domain I, bacterial / RuvA, C-terminal domain superfamily / RuvA N terminal domain / RuvA, C-terminal domain / Bacterial DNA recombination protein RuvA / Ubiquitin-associated (UBA) domain / RuvA domain 2-like / Helix-hairpin-helix domain / Helix-hairpin-helix DNA-binding motif, class 1 ...Holliday junction DNA helicase RuvA, C-terminal / DNA helicase, Holliday junction RuvA type, domain I, bacterial / RuvA, C-terminal domain superfamily / RuvA N terminal domain / RuvA, C-terminal domain / Bacterial DNA recombination protein RuvA / Ubiquitin-associated (UBA) domain / RuvA domain 2-like / Helix-hairpin-helix domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Helicase, Ruva Protein; domain 3 / Nucleic acid-binding proteins / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Holliday junction ATP-dependent DNA helicase RuvA / Holliday junction branch migration complex subunit RuvA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPrabu, J.R. / Thamotharan, S. / Khanduja, J.S. / Alipio, E.Z. / Kim, C.Y. / Waldo, G.S. / Terwilliger, T.C. / Segelke, B. / Lekin, T. / Toppani, D. ...Prabu, J.R. / Thamotharan, S. / Khanduja, J.S. / Alipio, E.Z. / Kim, C.Y. / Waldo, G.S. / Terwilliger, T.C. / Segelke, B. / Lekin, T. / Toppani, D. / Hung, L.W. / Yu, M. / Bursey, E. / Muniyappa, K. / Chandra, N.R. / Vijayan, M.
CitationJournal: ACTA CRYSTALLOGR.,SECT.F / Year: 2006
Title: Structure of Mycobacterium tuberculosis RuvA, a protein involved in recombination.
Authors: Prabu, J.R. / Thamotharan, S. / Khanduja, J.S. / Alipio, E.Z. / Kim, C.Y. / Waldo, G.S. / Terwilliger, T.C. / Segelke, B. / Lekin, T. / Toppani, D. / Hung, L.W. / Yu, M. / Bursey, E. / ...Authors: Prabu, J.R. / Thamotharan, S. / Khanduja, J.S. / Alipio, E.Z. / Kim, C.Y. / Waldo, G.S. / Terwilliger, T.C. / Segelke, B. / Lekin, T. / Toppani, D. / Hung, L.W. / Yu, M. / Bursey, E. / Muniyappa, K. / Chandra, N.R. / Vijayan, M.
History
DepositionMay 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Holliday junction ATP-dependent DNA helicase ruvA
B: Holliday junction ATP-dependent DNA helicase ruvA
C: Holliday junction ATP-dependent DNA helicase ruvA
D: Holliday junction ATP-dependent DNA helicase ruvA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2178
Polymers80,8494
Non-polymers3684
Water4,864270
1
A: Holliday junction ATP-dependent DNA helicase ruvA
B: Holliday junction ATP-dependent DNA helicase ruvA
C: Holliday junction ATP-dependent DNA helicase ruvA
D: Holliday junction ATP-dependent DNA helicase ruvA
hetero molecules

A: Holliday junction ATP-dependent DNA helicase ruvA
B: Holliday junction ATP-dependent DNA helicase ruvA
C: Holliday junction ATP-dependent DNA helicase ruvA
D: Holliday junction ATP-dependent DNA helicase ruvA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,43416
Polymers161,6988
Non-polymers7378
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)137.642, 137.642, 88.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
DetailsThe biological assembly is a Octamer generated from the tetramer in the asymmetric unit by the following symmetry operation. Symmetry: Y,X,-Z+1

-
Components

#1: Protein
Holliday junction ATP-dependent DNA helicase ruvA


Mass: 20212.203 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: ruvA / Plasmid: pET-28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P66744, UniProt: P9WGW3*PLUS, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.61 Å3/Da / Density % sol: 52.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Protein stock was buffered in 20 mM Tris-HCl at pH 8.0 with 100 mM sodium chloride and 10 mM b-ME. 0.1 M sodium succinate at pH 5.5 and 1.7 M ammonium sulfate was used as a precipitant, ...Details: Protein stock was buffered in 20 mM Tris-HCl at pH 8.0 with 100 mM sodium chloride and 10 mM b-ME. 0.1 M sodium succinate at pH 5.5 and 1.7 M ammonium sulfate was used as a precipitant, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 3, 2004
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→45 Å / Num. obs: 23937 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 14.1
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2325 / % possible all: 100

-
Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCdata collection
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1BVS

1bvs
PDB Unreleased entry


Resolution: 2.7→44.49 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2661258.69 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: MLF FUNCTION THROUGHOUT THE REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1157 4.8 %RANDOM
Rwork0.233 ---
obs0.233 23897 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.4038 Å2 / ksol: 0.347335 e/Å3
Displacement parametersBiso mean: 43.8 Å2
Baniso -1Baniso -2Baniso -3
1--7.28 Å20 Å20 Å2
2---7.28 Å20 Å2
3---14.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.7→44.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5265 0 24 270 5559
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.37
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg3.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.67
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.373 189 4.9 %
Rwork0.324 3634 -
obs--97.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2gol_xplor_par.txtgol_xplor_top.txt
X-RAY DIFFRACTION3water_rep.paramwater.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://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