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- PDB-1oyp: Crystal Structure of the phosphorolytic exoribonuclease RNase PH ... -

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Basic information

Entry
Database: PDB / ID: 1oyp
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
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 / 3' exoribonuclease family, domain 1 ...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: 2.76 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 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease PH
B: Ribonuclease PH
C: Ribonuclease PH
D: Ribonuclease PH
E: Ribonuclease PH
F: Ribonuclease PH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,43318
Polymers160,2816
Non-polymers1,15312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.310, 163.560, 166.800
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 PH / RNase PH / tRNA nucleotidyltransferase


Mass: 26713.441 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: P28619, tRNA nucleotidyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.58 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112.5 mg/mlprotein1drop
21.0 M1reservoirNH4HCO3
33.0 M1reservoir(NH4)2SO4

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.76→29.86 Å / Num. all: 37521 / Num. obs: 36616
Reflection
*PLUS
Highest resolution: 2.75 Å / Lowest resolution: 30 Å / Num. obs: 36688 / % possible obs: 99.2 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.097
Reflection shell
*PLUS
Highest resolution: 2.75 Å / Lowest resolution: 2.8 Å / % possible obs: 96.6 % / Redundancy: 4.9 % / Num. unique obs: 1753 / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 3.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.76→29.88 Å / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflection
Rfree0.3055 1841 4.9 %
Rwork0.2852 --
obs-36616 97.6 %
Refinement stepCycle: LAST / Resolution: 2.76→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10308 0 60 0 10368
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1570.75
X-RAY DIFFRACTIONc_scbond_it1.5451
X-RAY DIFFRACTIONc_mcangle_it2.0261
X-RAY DIFFRACTIONc_scangle_it2.4521.25
Refinement
*PLUS
Highest resolution: 2.75 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.306 / Rfactor Rwork: 0.285
Solvent computation
*PLUS
Displacement parameters
*PLUS

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