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- PDB-7vsb: E. coli Ribonuclease HI in complex with one Zn2+ (His124 N-delta ... -

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Basic information

Entry
Database: PDB / ID: 7vsb
TitleE. coli Ribonuclease HI in complex with one Zn2+ (His124 N-delta 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 (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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)35,3774
Polymers35,2462
Non-polymers1312
Water2,666148
1
A: Ribonuclease HI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6882
Polymers17,6231
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-36 kcal/mol
Surface area8600 Å2
MethodPISA
2
B: Ribonuclease HI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6882
Polymers17,6231
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-26 kcal/mol
Surface area8710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.174, 86.174, 80.112
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-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 (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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.11 Å3/Da / Density % sol: 41.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M sodium citrate tribasic dihydrate pH 5.6, 20% v/v 2-propanol, 20% w/v polyethylene glycol 4,000

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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: 1.84→48.5 Å / Num. obs: 26808 / % possible obs: 99.9 % / Redundancy: 10.9 % / Biso Wilson estimate: 21.06 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.041 / Rrim(I) all: 0.102 / Net I/σ(I): 17.1
Reflection shellResolution: 1.84→1.88 Å / Rmerge(I) obs: 0.384 / Num. unique obs: 1623 / CC1/2: 0.991 / Rpim(I) all: 0.179 / Rrim(I) all: 0.424

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4z0u

4z0u


Resolution: 1.84→48.5 Å / SU ML: 0.1998 / Cross valid method: FREE R-VALUE / σ(F): 0.77 / Phase error: 21.6046
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2214 2399 4.81 %
Rwork0.1847 47482 -
obs0.1865 26808 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.73 Å2
Refinement stepCycle: LAST / Resolution: 1.84→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2476 0 2 148 2626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00572581
X-RAY DIFFRACTIONf_angle_d0.74553501
X-RAY DIFFRACTIONf_chiral_restr0.0512366
X-RAY DIFFRACTIONf_plane_restr0.0043455
X-RAY DIFFRACTIONf_dihedral_angle_d18.819969
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.880.27431550.21052781X-RAY DIFFRACTION99.66
1.88-1.920.23731820.1962742X-RAY DIFFRACTION99.59
1.92-1.960.24611540.20252774X-RAY DIFFRACTION99.63
1.96-2.010.23981640.18722757X-RAY DIFFRACTION99.42
2.01-2.070.2311340.19272825X-RAY DIFFRACTION99.6
2.07-2.130.26561460.19352750X-RAY DIFFRACTION99.59
2.13-2.20.27151940.18822732X-RAY DIFFRACTION99.66
2.2-2.270.23221340.1862819X-RAY DIFFRACTION99.83
2.27-2.370.20141420.19262787X-RAY DIFFRACTION99.97
2.37-2.470.23871190.19242810X-RAY DIFFRACTION99.9
2.47-2.60.26851050.19842853X-RAY DIFFRACTION99.86
2.6-2.770.2447930.19942839X-RAY DIFFRACTION99.86
2.77-2.980.24081280.1982829X-RAY DIFFRACTION99.93
2.98-3.280.23561100.1892805X-RAY DIFFRACTION99.73
3.28-3.750.18721350.17122796X-RAY DIFFRACTION99.73
3.75-4.730.19441820.15962772X-RAY DIFFRACTION99.83
4.73-48.50.19321220.17972811X-RAY DIFFRACTION99.76

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