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- PDB-1ril: CRYSTAL STRUCTURE OF RIBONUCLEASE H FROM THERMUS THERMOPHILUS HB8... -

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Basic information

Entry
Database: PDB / ID: 1ril
TitleCRYSTAL STRUCTURE OF RIBONUCLEASE H FROM THERMUS THERMOPHILUS HB8 REFINED AT 2.8 ANGSTROMS RESOLUTION
ComponentsRIBONUCLEASE H
KeywordsHYDROLASE(ENDORIBONUCLEASE)
Function / homology
Function and homology information


DNA replication, removal of RNA primer / ribonuclease H / RNA-DNA hybrid ribonuclease 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 speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsIshikawa, K. / Okumura, M. / Katayanagi, K. / Kimura, S. / Kanaya, S. / Nakamura, H. / Morikawa, K.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Crystal structure of ribonuclease H from Thermus thermophilus HB8 refined at 2.8 A resolution.
Authors: Ishikawa, K. / Okumura, M. / Katayanagi, K. / Kimura, S. / Kanaya, S. / Nakamura, H. / Morikawa, K.
#1: Journal: Proteins / Year: 1993
Title: Crystallization and Preliminary Crystallographic Analysis of Ribonuclease H from Thermus Thermophilus Hb8
Authors: Okumura, M. / Ishikawa, K. / Kanaya, S. / Itaya, M. / Morikawa, K.
History
DepositionJan 14, 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 / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)18,7631
Polymers18,7631
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.700, 44.700, 314.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Atom site foot note1: RESIDUE 17 IS A CIS PROLINE.

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Components

#1: Protein RIBONUCLEASE H


Mass: 18763.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / References: UniProt: P29253, ribonuclease H
Sequence detailsTHE NUMBERING OF THE AMINO ACIDS CONFORMS TO THAT OF ESCHERICHIA COLI RNASE HI, IN ORDER TO ...THE NUMBERING OF THE AMINO ACIDS CONFORMS TO THAT OF ESCHERICHIA COLI RNASE HI, IN ORDER TO FACILITATE THE COMPARISON BETWEEN THE TWO ENZYMES. THERE IS A SINGLE INSERTION BETWEEN RESIDUES 80 AND 81, NUMBERED 80B.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal grow
*PLUS
pH: 9.8 / Method: unknown
Details: taken from Okumura, M. et al (1993). Proteins Struct. Funct. Genet., 15, 108-111.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118 mMTris-HCl1drop
25 mMdithiothreitol1drop
350 mMTris-HCl1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 4766 / % possible obs: 89 % / Observed criterion σ(I): 1 / Num. measured all: 46156 / Rmerge(I) obs: 0.093

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.8→8 Å / σ(F): 1
Details: THERE ARE TWO REGIONS OF LOW (OR NO) DENSITY, CONSISTING OF MET -4 - PRO 1 (N TERMINUS) AND PRO 148 - ALA 161 (C TERMINUS).
RfactorNum. reflection
obs0.205 4766
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1175 0 0 0 1175
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.02
X-RAY DIFFRACTIONp_angle_d0.0480.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0550.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.9131.5
X-RAY DIFFRACTIONp_mcangle_it2.9082
X-RAY DIFFRACTIONp_scbond_it1.8962
X-RAY DIFFRACTIONp_scangle_it2.8012.5
X-RAY DIFFRACTIONp_plane_restr0.0160.02
X-RAY DIFFRACTIONp_chiral_restr0.2080.15
X-RAY DIFFRACTIONp_singtor_nbd0.2030.3
X-RAY DIFFRACTIONp_multtor_nbd0.2520.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2180.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor33
X-RAY DIFFRACTIONp_staggered_tor2815
X-RAY DIFFRACTIONp_orthonormal_tor28.220
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 8 Å / Num. reflection obs: 4766 / σ(F): 1 / Rfactor obs: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS

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