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- PDB-1kvb: E. COLI RIBONUCLEASE HI D134H MUTANT -

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Basic information

Entry
Database: PDB / ID: 1kvb
TitleE. COLI RIBONUCLEASE HI D134H MUTANT
ComponentsRIBONUCLEASE H
KeywordsENDORIBONUCLEASE / HYDROLASE / MUTANT
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 / Resolution: 1.9 Å
AuthorsKashiwagi, T. / Jeanteur, D. / Haruki, M. / Katayanagi, K. / Kanaya, S. / Morikawa, K.
Citation
Journal: Protein Eng. / Year: 1996
Title: Proposal for new catalytic roles for two invariant residues in Escherichia coli ribonuclease HI.
Authors: Kashiwagi, T. / Jeanteur, D. / Haruki, M. / Katayanagi, K. / Kanaya, S. / Morikawa, K.
#1: Journal: Proteins / Year: 1993
Title: Crystal Structure of Escherichia Coli Rnase Hi in Complex with Mg2+ at 2.8 A Resolution: Proof for a Single Mg(2+)-Binding Site
Authors: Katayanagi, K. / Okumura, M. / Morikawa, K.
#2: Journal: J.Mol.Biol. / Year: 1992
Title: Structural Details of Ribonuclease H from Escherichia Coli as Refined to an Atomic Resolution
Authors: Katayanagi, K. / Miyagawa, M. / Matsushima, M. / Ishikawa, M. / Kanaya, S. / Nakamura, H. / Ikehara, M. / Matsuzaki, T. / Morikawa, K.
#3: Journal: Science / Year: 1990
Title: Structure of Ribonuclease H Phased at 2 A Resolution by MAD Analysis of the Selenomethionyl Protein
Authors: Yang, W. / Hendrickson, W.A. / Crouch, R.J. / Satow, Y.
#4: Journal: Nature / Year: 1990
Title: Three-Dimensional Structure of Ribonuclease H from E. Coli
Authors: Katayanagi, K. / Miyagawa, M. / Matsushima, M. / Ishikawa, M. / Kanaya, S. / Ikehara, M. / Matsuzaki, T. / Morikawa, K.
History
DepositionOct 4, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 1.4Nov 3, 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 1.5Feb 14, 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 H


Theoretical massNumber of molelcules
Total (without water)17,6461
Polymers17,6461
Non-polymers00
Water3,189177
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.790, 86.700, 37.630
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 H / RNASE H


Mass: 17646.057 Da / Num. of mol.: 1 / Mutation: D134H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MIC3001 / Plasmid: PJAL134H / Gene (production host): RNHA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7Y4, ribonuclease H
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.5 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 9 / Method: vapor diffusion, hanging drop / Details: macro-seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 mg/mlprotein1drop
20.2 MTris-HCl1drop
30.4 MTris-HCl1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: May 13, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 9295 / % possible obs: 81.9 % / Observed criterion σ(I): 0.5 / Redundancy: 3.07 % / Rmerge(I) obs: 0.077
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. measured all: 28545
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.93 Å / % possible obs: 68 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
PROLSQrefinement
X-PLOR3.1refinement
MADNESdata reduction
X-PLOR3.1phasing
RefinementResolution: 1.9→6 Å / σ(F): 1
Details: IDEAL BOND LENGTHS AND ANGLES USED DURING REFINEMENT: HENDRICKSON AND KONNERT INITIAL REFINEMENTS WERE DONE WITH X-PLOR 3.1 BY BRUNGER.
RfactorNum. reflection
Rwork0.197 -
obs-8908
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1254 0 0 177 1431
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0290.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0370.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.2961.5
X-RAY DIFFRACTIONp_mcangle_it2.1052
X-RAY DIFFRACTIONp_scbond_it1.712
X-RAY DIFFRACTIONp_scangle_it2.5312.5
X-RAY DIFFRACTIONp_plane_restr0.0120.02
X-RAY DIFFRACTIONp_chiral_restr0.1590.15
X-RAY DIFFRACTIONp_singtor_nbd0.1830.3
X-RAY DIFFRACTIONp_multtor_nbd0.2080.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2030.3
X-RAY DIFFRACTIONp_planar_tor2.13
X-RAY DIFFRACTIONp_staggered_tor1915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor39.320
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS

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