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- PDB-1oys: Crystal Structure of the Phosphorolytic Exoribonuclease RNase PH ... -

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Basic information

Entry
Database: PDB / ID: 1oys
TitleCrystal Structure of the Phosphorolytic Exoribonuclease RNase PH from Bacillus subtilis
ComponentsRibonuclease PH
KeywordsTRANSFERASE / tRNA processing
Function / homology
Function and homology information


tRNA nucleotidyltransferase / tRNA nucleotidyltransferase activity / rRNA 3'-end processing / rRNA catabolic process / tRNA processing / 3'-5'-RNA exonuclease activity / tRNA binding / RNA binding
Similarity search - Function
Ribonuclease PH, bacterial-type / Ribonuclease PH, conserved site / Ribonuclease PH signature. / GHMP Kinase, N-terminal domain / : / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily ...Ribonuclease PH, bacterial-type / Ribonuclease PH, conserved site / Ribonuclease PH signature. / GHMP Kinase, N-terminal domain / : / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily / 3' exoribonuclease family, domain 1 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHarlow, L.S. / Kadziola, A. / Jensen, K.F. / Larsen, S.
CitationJournal: Protein Sci. / Year: 2004
Title: Crystal structure of the phosphorolytic exoribonuclease RNase PH from Bacillus subtilis and implications for its quaternary structure and tRNA binding.
Authors: Harlow, L.S. / Kadziola, A. / Jensen, K.F. / Larsen, S.
History
DepositionApr 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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 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 PH


Theoretical massNumber of molelcules
Total (without water)26,6261
Polymers26,6261
Non-polymers00
Water00
1
A: Ribonuclease PH

A: Ribonuclease PH


Theoretical massNumber of molelcules
Total (without water)53,2522
Polymers53,2522
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)63.230, 63.230, 203.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Ribonuclease PH / RNase PH / tRNA nucleotidyltransferase


Mass: 26626.244 Da / Num. of mol.: 1 / Mutation: R68Q,R73Q,R76Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: RPH / Production host: Escherichia coli (E. coli) / References: UniProt: P28619, tRNA nucleotidyltransferase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.47 Å3/Da / Density % sol: 72.29 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.2 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115.3 mg/mlprotein1drop
21 Msodium citrate1reservoirpH6.2
310 %PEG4001reservoir

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 16768
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 98.8 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.44 Å / % possible obs: 100 % / Redundancy: 5.5 % / Num. unique obs: 817 / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→20 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2841 848 5 %
Rwork0.2583 --
obs-16722 98.5 %
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1620 0 0 0 1620
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_scbond_it2.4552
X-RAY DIFFRACTIONc_mcangle_it1.2182
X-RAY DIFFRACTIONc_scangle_it3.7362.5
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.284 / Rfactor Rwork: 0.258
Solvent computation
*PLUS
Displacement parameters
*PLUS

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