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- PDB-2z1j: Crystal structure of E.coli RNase HI surface charged mutant(Q4R/T... -

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Basic information

Entry
Database: PDB / ID: 2z1j
TitleCrystal structure of E.coli RNase HI surface charged mutant(Q4R/T40E/Q72H/Q76K/Q80E/T92K/Q105K/Q113R/Q115K/N143K/T145K)
ComponentsRibonuclease HI
KeywordsHYDROLASE / RNase HI / thermostability / surface-charge residue
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 / : / Ribonuclease H-like superfamily/Ribonuclease H / RNase H / RNase H type-1 domain profile. / Ribonuclease H domain / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsYou, D.J. / Fukuchi, S. / Nishikawa, K. / Koga, Y. / Takano, K. / Kanaya, S.
CitationJournal: J.Biochem.(Tokyo) / Year: 2007
Title: Protein Thermostabilization Requires a Fine-tuned Placement of Surface-charged Residues
Authors: You, D.-J. / Fukuchi, S. / Nishikawa, K. / Koga, Y. / Takano, K. / Kanaya, S.
History
DepositionMay 8, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 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


Theoretical massNumber of molelcules
Total (without water)17,7951
Polymers17,7951
Non-polymers00
Water77543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.273, 85.273, 51.024
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 17794.529 Da / Num. of mol.: 1
Mutation: Q4R/T40E/Q72H/Q76K/Q80E/T92K/Q105K/Q113R/Q115K/N143K/T145K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET25b / Production host: Escherichia coli (E. coli) / Strain (production host): MIC2067(DE3) / References: UniProt: P0A7Y4, ribonuclease H
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 3.01 Å3/Da / Density % sol: 59.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100mM HEPES-NaOH, 15-25% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 11, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 9722 / % possible obs: 99.2 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 23.8
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 1.9 / % possible all: 92.5

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2RN2

2rn2


Resolution: 2.38→41.98 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1089803.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.238 468 5.3 %RANDOM
Rwork0.208 ---
obs0.208 8828 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.3662 Å2 / ksol: 0.337065 e/Å3
Displacement parametersBiso mean: 38.8 Å2
Baniso -1Baniso -2Baniso -3
1-2 Å25.58 Å20 Å2
2--2 Å20 Å2
3----4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.38→41.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 0 43 1260
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d1.13
X-RAY DIFFRACTIONc_mcbond_it1.061.5
X-RAY DIFFRACTIONc_mcangle_it1.72
X-RAY DIFFRACTIONc_scbond_it1.962
X-RAY DIFFRACTIONc_scangle_it3.022.5
LS refinement shellResolution: 2.38→2.53 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.302 76 5.4 %
Rwork0.234 1343 -
obs--99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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