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- PDB-7ess: Structure-guided studies of the Holliday junction resolvase RuvX ... -

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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 / YqgF/RNase H-like domain / Likely ribonuclease with RNase H fold. / YqgF/RNase H-like domain superfamily / Nucleotidyltransferase; domain 5 / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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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

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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

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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 %

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