[English] 日本語
Yorodumi
- PDB-5yww: Archael RuvB-like Holiday junction helicase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yww
TitleArchael RuvB-like Holiday junction helicase
ComponentsNucleotide binding protein PINc
KeywordsHYDROLASE / ATPase / Helicase
Function / homology
Function and homology information


DNA recombination / DNA helicase / four-way junction helicase activity / hydrolase activity / DNA repair / DNA binding / ATP binding
Similarity search - Function
: / Type II/IV secretion system protein / Type II/IV secretion system protein / 5'-nuclease / Large family of predicted nucleotide-binding domains / PIN domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Holliday junction branch migration ATPase PINA
Similarity search - Component
Biological speciesSulfolobus islandicus REY15A (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsZhai, B. / Yuan, Z. / Han, X. / DuPrez, K. / Shen, Y. / Fan, L.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: The archaeal ATPase PINA interacts with the helicase Hjm via its carboxyl terminal KH domain remodeling and processing replication fork and Holliday junction.
Authors: Zhai, B. / DuPrez, K. / Han, X. / Yuan, Z. / Ahmad, S. / Xu, C. / Gu, L. / Ni, J. / Fan, L. / Shen, Y.
History
DepositionNov 30, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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: Nucleotide binding protein PINc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2452
Polymers57,1531
Non-polymers921
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-0 kcal/mol
Surface area23790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.116, 74.766, 107.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

-
Components

#1: Protein Nucleotide binding protein PINc


Mass: 57153.012 Da / Num. of mol.: 1 / Mutation: R147K, I199S, R206A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus islandicus REY15A (archaea) / Strain: REY15A / Gene: SiRe_1432 / Production host: Escherichia coli (E. coli) / References: UniProt: F0NID4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.43 Å3/Da / Density % sol: 49.42 %
Crystal growTemperature: 287 K / Method: evaporation
Details: 0.1M Bis-tris pH 6.5, 20% PEG monomethyl ether 5000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 24438 / % possible obs: 99.4 % / Redundancy: 5.8 % / Rpim(I) all: 0.046 / Net I/σ(I): 32.38
Reflection shellResolution: 2.33→2.39 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.44 / Rpim(I) all: 0.414 / % possible all: 97.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F4H

5f4h


Resolution: 2.33→19.87 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.94 / SU B: 8.336 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.404 / ESU R Free: 0.245 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23642 1899 8.3 %RANDOM
Rwork0.20719 ---
obs0.20966 21020 93.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 55.265 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.33→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3680 0 6 79 3765
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193737
X-RAY DIFFRACTIONr_bond_other_d0.0060.023583
X-RAY DIFFRACTIONr_angle_refined_deg1.5771.9815062
X-RAY DIFFRACTIONr_angle_other_deg1.02238269
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4555483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.38825.105143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.52315668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9781517
X-RAY DIFFRACTIONr_chiral_restr0.0890.2612
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024111
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02686
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5715.5931938
X-RAY DIFFRACTIONr_mcbond_other3.575.591937
X-RAY DIFFRACTIONr_mcangle_it5.4858.3752419
X-RAY DIFFRACTIONr_mcangle_other5.4848.3782420
X-RAY DIFFRACTIONr_scbond_it3.7395.9121799
X-RAY DIFFRACTIONr_scbond_other3.7225.9121799
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9398.692644
X-RAY DIFFRACTIONr_long_range_B_refined8.29665.2973926
X-RAY DIFFRACTIONr_long_range_B_other8.29665.2983927
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.329→2.389 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 130 -
Rwork0.29 1309 -
obs--81.21 %

+
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