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- PDB-1jxb: I53A, a point mutant of the cysteine-free variant of E. coli Rnase HI -

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Basic information

Entry
Database: PDB / ID: 1jxb
TitleI53A, a point mutant of the cysteine-free variant of E. coli Rnase HI
ComponentsRibonuclease HI
KeywordsHYDROLASE / MIXED ALPHA/BETA / 4-HELIX BUNDLE
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: 1.6 Å
AuthorsSpudich, G. / Lorenz, S. / Marqusee, S.
CitationJournal: Protein Sci. / Year: 2002
Title: Propagation of a single destabilizing mutation throughout the Escherichia coli ribonuclease HI native state.
Authors: Spudich, G. / Lorenz, S. / Marqusee, S.
History
DepositionSep 6, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)17,4851
Polymers17,4851
Non-polymers00
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.867, 40.830, 85.016
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 17484.725 Da / Num. of mol.: 1 / Mutation: I53A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pSM101 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7Y4, ribonuclease H
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 32.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3350, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mMHEPES1droppH7.5
210 %PEG33501drop
34 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 19, 1999
RadiationMonochromator: SINGLE WAVELENGTH / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→25 Å / Num. all: 207864 / Num. obs: 34997 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.6→1.66 Å / % possible all: 91.4
Reflection
*PLUS
Lowest resolution: 25 Å / Rmerge(I) obs: 0.062

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→12.5 Å
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1666 11.07 %RANDOM
Rwork0.207 ---
all-26389 --
obs-15049 --
Refinement stepCycle: LAST / Resolution: 1.6→12.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1208 0 0 161 1369
Refinement
*PLUS
Highest resolution: 1.6 Å / % reflection Rfree: 11.07 % / Rfactor obs: 0.207
Solvent computation
*PLUS
Displacement parameters
*PLUS

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