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- PDB-1gob: COOPERATIVE STABILIZATION OF ESCHERICHIA COLI RIBONUCLEASE HI BY ... -

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Basic information

Entry
Database: PDB / ID: 1gob
TitleCOOPERATIVE STABILIZATION OF ESCHERICHIA COLI RIBONUCLEASE HI BY INSERTION OF GLY-80B AND GLY-77-> ALA SUBSTITUTION
ComponentsRIBONUCLEASE H
KeywordsHYDROLASE(ENDORIBONUCLEASE)
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: 2 Å
AuthorsIshikawa, K. / Kimura, S. / Nakamura, H. / Morikawa, K. / Kanaya, S.
Citation
Journal: Biochemistry / Year: 1993
Title: Cooperative stabilization of Escherichia coli ribonuclease HI by insertion of Gly-80b and Gly-77-->Ala substitution.
Authors: Ishikawa, K. / Nakamura, H. / Morikawa, K. / Kimura, S. / Kanaya, S.
#1: 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.
#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: 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.
History
DepositionMay 10, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: 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 7, 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 ON SHEET RECORD *S1* THESE STRANDS ARE DEFINED AS FOLLOWS IN THE PAPER (KATAYANAGI ET AL. ...SHEET ON SHEET RECORD *S1* THESE STRANDS ARE DEFINED AS FOLLOWS IN THE PAPER (KATAYANAGI ET AL. NATURE (1990) VOL.347 PP306-309). 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
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.350, 86.800, 35.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUE PRO 17 IS A CIS PROLINE.

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Components

#1: Protein RIBONUCLEASE H


Mass: 17637.023 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


Mass: 18.015 Da / Num. of mol.: 114 / 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: 1.98 Å3/Da / Density % sol: 37.92 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 9 / Method: vapor diffusion
Details: used to seeding, Ishikawa, K., (1993) Protein Eng., 6, 85.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13-4 mg/mlprotein1drop
250 mMTris-HCl1drop
3200 mMTris-HCl1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2→6 Å / σ(F): 1 /
RfactorNum. reflection
obs0.191 6941
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1239 0 0 114 1353
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.015
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 6 Å / Num. reflection obs: 6941 / σ(F): 1 / Rfactor obs: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_angle_d / Dev ideal: 0.034

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