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- PDB-7vse: E. coli Ribonuclease HI in complex one Zn2+ (His124 N-epsilon binding) -

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Basic information

Entry
Database: PDB / ID: 7vse
TitleE. coli Ribonuclease HI in complex one Zn2+ (His124 N-epsilon binding)
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 K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 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

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Assembly

Deposited unit
A: Ribonuclease HI
B: Ribonuclease HI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8539
Polymers35,2462
Non-polymers6077
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-35 kcal/mol
Surface area8790 Å2
MethodPISA
2
B: Ribonuclease HI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8774
Polymers17,6231
Non-polymers2543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-35 kcal/mol
Surface area8390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.650, 64.586, 79.104
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Space group name HallP2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2

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Components

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


Mass: 17622.998 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.2 Å3/Da / Density % sol: 44.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2 M ammonium sulfate, 0.1 M sodium acetate trihydrate pH 4.6, 30% w/v polyethylene glycol monomethyl ether 2,000

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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: 2.08→48.13 Å / Num. obs: 35934 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 36.23 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.046 / Rrim(I) all: 0.086 / Net I/σ(I): 13.6
Reflection shellResolution: 2.08→2.14 Å / Rmerge(I) obs: 0.354 / Num. unique obs: 1463 / CC1/2: 0.96 / Rpim(I) all: 0.215 / Rrim(I) all: 0.415 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4z0u

4z0u


Resolution: 2.08→48.13 Å / SU ML: 0.3067 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 31.6868
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2763 1664 4.63 %
Rwork0.2299 34270 -
obs0.2321 35934 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.26 Å2
Refinement stepCycle: LAST / Resolution: 2.08→48.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2476 0 28 89 2593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312579
X-RAY DIFFRACTIONf_angle_d0.59693492
X-RAY DIFFRACTIONf_chiral_restr0.0394362
X-RAY DIFFRACTIONf_plane_restr0.0042449
X-RAY DIFFRACTIONf_dihedral_angle_d16.0838961
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.140.31211410.32732839X-RAY DIFFRACTION99.7
2.14-2.210.32651490.30892861X-RAY DIFFRACTION99.93
2.21-2.290.2871260.3142859X-RAY DIFFRACTION99.87
2.29-2.380.41191180.30152904X-RAY DIFFRACTION99.87
2.38-2.490.39361440.29822865X-RAY DIFFRACTION99.87
2.49-2.620.36431780.27292819X-RAY DIFFRACTION99.9
2.62-2.780.34311470.27722858X-RAY DIFFRACTION99.93
2.79-30.24871360.25042851X-RAY DIFFRACTION99.87
3-3.30.28651340.24392868X-RAY DIFFRACTION99.44
3.3-3.780.25551000.19922877X-RAY DIFFRACTION98.97
3.78-4.760.20751300.18882839X-RAY DIFFRACTION98.8
4.76-48.130.25381610.18222830X-RAY DIFFRACTION99.2

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