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- PDB-1lav: STABILIZATION OF ESCHERICHIA COLI RIBONUCLEASE HI BY CAVITY-FILLI... -

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Basic information

Entry
Database: PDB / ID: 1lav
TitleSTABILIZATION OF ESCHERICHIA COLI RIBONUCLEASE HI BY CAVITY-FILLING MUTATIONS WITHIN A HYDROPHOBIC CORE
ComponentsRIBONUCLEASE H
KeywordsHYDROLASE
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 / Ribonuclease H domain / RNase H type-1 domain profile. / 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: 1.8 Å
AuthorsIshikawa, K. / Nakamura, H. / Morikawa, K. / Kanaya, S.
Citation
Journal: Biochemistry / Year: 1993
Title: Stabilization of Escherichia coli ribonuclease HI by cavity-filling mutations within a hydrophobic core.
Authors: Ishikawa, K. / Nakamura, H. / Morikawa, K. / Kanaya, S.
#1: Journal: Protein Eng. / Year: 1993
Title: Structural Study of Mutants of Escherichia Coli Ribonuclease Hi with Enhanced Thermostability
Authors: Ishikawa, K. / Kimura, S. / Kanaya, S. / Morikawa, K. / Nakamura, H.
#2: Journal: J.Mol.Biol. / Year: 1992
Title: Structural Details of Ribonuclease H from Escherichia Coli as Refined at an Atomic Resolution
Authors: Katayanagi, K. / Miyagawa, M. / Matsushima, M. / Ishikawa, M. / Kanaya, S. / Nakamura, H. / Ikehara, M. / Matsuzaki, T. / Morikawa, K.
#3: 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
DepositionMay 10, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 700SHEET THE STRANDS IN THE SHEET RECORD BELOW ARE DEFINED AS FOLLOWS IN THE PAPER (KATAYANAGI ET AL. ...SHEET THE STRANDS IN THE SHEET RECORD BELOW ARE DEFINED AS FOLLOWS IN THE PAPER (KATAYANAGI ET AL. NATURE (1990) VOL. 347, PP. 306-309). STRAND 1 (RIGHT ARROW) BETA C STRAND 2 (RIGHT ARROW) BETA B STRAND 3 (RIGHT ARROW) BETA A STRAND 4 (RIGHT ARROW) BETA D STRAND 5 (RIGHT ARROW) BETA E

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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)17,6371
Polymers17,6371
Non-polymers00
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.150, 86.930, 35.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO 17

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Components

#1: Protein RIBONUCLEASE H /


Mass: 17637.025 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P0A7Y4, ribonuclease H
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 36.22 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 9 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17.5 mg/mlprotein1drop
250 mMTris-HCl1drop
3200 mMTris-HCl1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.8→6 Å / σ(F): 1 /
RfactorNum. reflection
obs0.183 10201
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1239 0 0 117 1356
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0350.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0510.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.2051.5
X-RAY DIFFRACTIONp_mcangle_it1.8962
X-RAY DIFFRACTIONp_scbond_it2.0962
X-RAY DIFFRACTIONp_scangle_it3.1942.5
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.1620.15
X-RAY DIFFRACTIONp_singtor_nbd0.1860.3
X-RAY DIFFRACTIONp_multtor_nbd0.2080.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2530.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.43
X-RAY DIFFRACTIONp_staggered_tor19.415
X-RAY DIFFRACTIONp_orthonormal_tor29.620
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 6 Å / Num. reflection obs: 10201 / σ(F): 1 / Rfactor obs: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS

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