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- PDB-7vsc: E. coli Ribonuclease HI in complex with one Mg2+ (1) -

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Basic information

Entry
Database: PDB / ID: 7vsc
TitleE. coli Ribonuclease HI in complex with one Mg2+ (1)
ComponentsRibonuclease HI
KeywordsHYDROLASE / endonuclease / metalloenzyme
Function / homology
Function and homology information


DNA replication, removal of RNA primer / ribonuclease H / RNA-DNA hybrid ribonuclease activity / endonuclease activity / nucleic acid binding / magnesium ion binding / cytoplasm
Similarity search - Function
Ribonuclease HI / : / RNase H / RNase H type-1 domain profile. / Ribonuclease H domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsLiao, Z. / Oyama, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21H02120 Japan
Japan Science and TechnologyJPMJTM20NM Japan
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Pivotal role of a conserved histidine in Escherichia coli ribonuclease HI as proposed by X-ray crystallography.
Authors: Liao, Z. / Oyama, T. / Kitagawa, Y. / Katayanagi, K. / Morikawa, K. / Oda, M.
History
DepositionOct 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
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: Ribonuclease HI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8645
Polymers17,6231
Non-polymers2414
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-16 kcal/mol
Surface area8670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.998, 61.998, 80.138
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Space group name HallP4cw2c
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+1/4
#8: -y,-x,-z+3/4

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Components

#1: Protein Ribonuclease HI / RNase HI / Ribonuclease H / RNase H


Mass: 17622.998 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: rnhA, dasF, herA, rnh, sdrA, b0214, JW0204 / Production host: Escherichia coli (E. coli) / Strain (production host): MIC3001 / References: UniProt: P0A7Y4, ribonuclease H
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.18 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Sodium acetate trihydrate, 0.1 M sodium cacodylate trihydrate pH 6.5, 30% w/v polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→49.04 Å / Num. obs: 14230 / % possible obs: 99.2 % / Redundancy: 12.4 % / Biso Wilson estimate: 28.78 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.056 / Rrim(I) all: 0.144 / Net I/σ(I): 11.2
Reflection shellResolution: 1.83→1.87 Å / Rmerge(I) obs: 1.417 / Num. unique obs: 844 / CC1/2: 0.94 / Rpim(I) all: 0.58 / Rrim(I) all: 1.533

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1g15

1g15


Resolution: 1.83→49.04 Å / SU ML: 0.2159 / Cross valid method: FREE R-VALUE / σ(F): 0.36 / Phase error: 32.6105
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2503 1305 5.01 %
Rwork0.203 24746 -
obs0.2052 14230 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.26 Å2
Refinement stepCycle: LAST / Resolution: 1.83→49.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1237 0 12 83 1332
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00451309
X-RAY DIFFRACTIONf_angle_d0.62881777
X-RAY DIFFRACTIONf_chiral_restr0.0419183
X-RAY DIFFRACTIONf_plane_restr0.0037229
X-RAY DIFFRACTIONf_dihedral_angle_d16.7663489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.90.31191600.30112708X-RAY DIFFRACTION97.78
1.9-1.990.3651070.25842740X-RAY DIFFRACTION98.04
1.99-2.090.32041380.23382751X-RAY DIFFRACTION98.5
2.1-2.230.27881740.21952697X-RAY DIFFRACTION98.25
2.23-2.40.2621510.21642762X-RAY DIFFRACTION99.49
2.4-2.640.32181350.22732775X-RAY DIFFRACTION99.25
2.64-3.020.23981320.22492785X-RAY DIFFRACTION99.49
3.02-3.810.20431780.18832732X-RAY DIFFRACTION99.42
3.81-49.040.24291300.17132796X-RAY DIFFRACTION99.69

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