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- PDB-1r6m: Crystal Structure Of The tRNA Processing Enzyme Rnase pH From Pse... -

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Basic information

Entry
Database: PDB / ID: 1r6m
TitleCrystal Structure Of The tRNA Processing Enzyme Rnase pH From Pseudomonas Aeruginosa In Complex With Phosphate
ComponentsRibonuclease PH
KeywordsTRANSFERASE / BETA-ALPHA-BETA-ALPHA FOLD / HEXAMER / PHOSPHATE BOUND
Function / homology
Function and homology information


tRNA nucleotidyltransferase / tRNA nucleotidyltransferase activity / rRNA catabolic process / tRNA processing / rRNA 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
PHOSPHATE ION / Ribonuclease PH
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / difference Fourier / Resolution: 2 Å
AuthorsChoi, J.M. / Park, E.Y. / Kim, J.H. / Chang, S.K. / Cho, Y.
CitationJournal: J.BIOL.CHEM. / Year: 2004
Title: Probing the functional importance of the hexameric ring structure of RNase PH
Authors: Choi, J.M. / Park, E.Y. / Kim, J.H. / Chang, S.K. / Cho, Y.
History
DepositionOct 15, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 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

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Assembly

Deposited unit
A: Ribonuclease PH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7782
Polymers25,6831
Non-polymers951
Water3,441191
1
A: Ribonuclease PH
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)154,66912
Polymers154,0996
Non-polymers5706
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation16_544y+1/3,x-1/3,-z-1/31
crystal symmetry operation17_554x-y+1/3,-y+2/3,-z-1/31
crystal symmetry operation18_654-x+4/3,-x+y+2/3,-z-1/31
Buried area17190 Å2
ΔGint-67 kcal/mol
Surface area52720 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)110.202, 110.202, 116.284
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsThe biological assembly is a hexamer generated from the monomer in the asymmetric unit by the operations; ( -y, x-y, z ), (-x+y, -x, z), (y, x, -z), (x-y, -y , -z) and (-x, -x+y, -z)

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Components

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


Mass: 25683.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: RPH / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: P50597, tRNA nucleotidyltransferase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Ammonium phosphate, citrate, sodium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
25 mMTris-HCl1droppH8.0
3150 mM1dropNaCl
45 mMdithiothreitol1drop
51.2 Mammonium sulfate1reservoir
60.1 M1reservoirNaCl
70.2 MCHES1reservoirpH9.5

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.1272 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: May 28, 2003
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1272 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 120641 / Num. obs: 18518 / % possible obs: 94.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2→2.07 Å / % possible all: 89
Reflection
*PLUS
Num. measured all: 120641 / Rmerge(I) obs: 0.039
Reflection shell
*PLUS
% possible obs: 89 % / Rmerge(I) obs: 0.332

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: difference Fourier / Resolution: 2→24.59 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 755476.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1007 5.9 %RANDOM
Rwork0.226 ---
obs0.226 17144 92.6 %-
all-17505 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.0311 Å2 / ksol: 0.366637 e/Å3
Displacement parametersBiso mean: 37.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å23.94 Å20 Å2
2--1.28 Å20 Å2
3----2.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2→24.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1782 0 5 191 1978
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_mcbond_it1.71.5
X-RAY DIFFRACTIONc_mcangle_it2.462
X-RAY DIFFRACTIONc_scbond_it2.412
X-RAY DIFFRACTIONc_scangle_it3.322.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.34 172 6.7 %
Rwork0.304 2392 -
obs--84.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PO4.PARAMPO4.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.279 / Rfactor Rwork: 0.227 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73

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