[English] 日本語
Yorodumi
- PDB-7ess: Structure-guided studies of the Holliday junction resolvase RuvX ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ess
TitleStructure-guided studies of the Holliday junction resolvase RuvX provide novel insights into ATP-stimulated cleavage of branched DNA and RNA substrates
ComponentsPutative pre-16S rRNA nuclease
KeywordsDNA BINDING PROTEIN / Holliday junction / Holliday junction resolvases / ATPase
Function / homology
Function and homology information


rRNA 5'-end processing / nuclease activity / Hydrolases; Acting on ester bonds / cytosol
Similarity search - Function
Putative pre-16S rRNA nuclease / Holliday junction resolvase / YqgF/RNase H-like domain / Likely ribonuclease with RNase H fold. / YqgF/RNase H-like domain superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
Putative pre-16S rRNA nuclease
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsThakur, M. / Mohan, D. / Singh, A.K. / Agarwal, A. / Gopal, B. / Muniyappa, K.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/CoE/34/SP15232/2015 India
Science and Engineering Research Board (SERB)IR/SO/LU-003/2010 India
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Novel insights into ATP-Stimulated Cleavage of branched DNA and RNA Substrates through Structure-Guided Studies of the Holliday Junction Resolvase RuvX.
Authors: Thakur, M. / Mohan, D. / Singh, A.K. / Agarwal, A. / Gopal, B. / Muniyappa, K.
History
DepositionMay 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Advisory / Database references
Category: citation / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative pre-16S rRNA nuclease
B: Putative pre-16S rRNA nuclease


Theoretical massNumber of molelcules
Total (without water)36,1852
Polymers36,1852
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-19 kcal/mol
Surface area13740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.490, 42.580, 58.110
Angle α, β, γ (deg.)90.000, 114.450, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Putative pre-16S rRNA nuclease


Mass: 18092.498 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: Rv2554c, MTCY159.02 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WGV7, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 1.83 Å3/Da / Density % sol: 32.73 %
Crystal growTemperature: 300 K / Method: batch mode / pH: 7
Details: 0.1 M Bis-Tris propane, pH 7.0 and 2.4 M sodium malonate, pH 7.0
PH range: 7

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Mar 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→53.477 Å / Num. obs: 19756 / % possible obs: 99.3 % / Redundancy: 4.7 % / Rpim(I) all: 0.034 / Rrim(I) all: 0.075 / Rsym value: 0.067 / Net I/av σ(I): 8.1 / Net I/σ(I): 13.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.93-2.044.30.3252.227720.1710.3680.32596.9
2.04-2.164.50.2293.127040.120.2590.22999
2.16-2.314.60.169425640.0850.190.16999.6
2.31-2.494.70.1215.723900.0610.1350.12199.7
2.49-2.734.80.0897.921870.0450.10.08999.8
2.73-3.054.80.06710.120050.0340.0750.067100
3.05-3.534.80.04414.617780.0220.0490.044100
3.53-4.324.90.04114.814970.020.0460.041100
4.32-6.114.80.04113.911840.020.0460.041100
6.11-53.4774.40.0369.56750.0210.0420.03699.9

-
Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
REFMAC5.8.0222refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VHX

1vhx


Resolution: 1.93→52.95 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2259 976 4.9 %RANDOM
Rwork0.1809 ---
obs0.183 18777 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.24 Å2 / Biso mean: 22.757 Å2 / Biso min: 10.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0 Å2-0.53 Å2
2--0.78 Å20 Å2
3---0.13 Å2
Refinement stepCycle: final / Resolution: 1.93→52.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2208 0 0 185 2393
Biso mean---33.17 -
Num. residues----294
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0152236
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172046
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.7643034
X-RAY DIFFRACTIONr_angle_other_deg3.6311.6994796
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4375302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.96713.06198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.59415306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4441540
X-RAY DIFFRACTIONr_chiral_restr0.0710.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212634
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02342
LS refinement shellResolution: 1.931→1.981 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 80 -
Rwork0.221 1306 -
all-1386 -
obs--97.06 %

+
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