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- PDB-1uds: Crystal structure of the tRNA processing enzyme RNase PH R126A mu... -

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Basic information

Entry
Database: PDB / ID: 1uds
TitleCrystal structure of the tRNA processing enzyme RNase PH R126A mutant from Aquifex aeolicus
ComponentsRibonuclease PH
KeywordsTRANSFERASE / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
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 / 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
PHOSPHATE ION / Ribonuclease PH
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsIshii, R. / Nureki, O. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal Structure of the tRNA Processing Enzyme RNase PH from Aquifex aeolicus
Authors: Ishii, R. / Nureki, O. / Yokoyama, S.
History
DepositionMay 2, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6094
Polymers28,3221
Non-polymers2873
Water1,71195
1
A: Ribonuclease PH
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)171,65724
Polymers169,9346
Non-polymers1,72318
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_555-x+y,y,-z+1/21
crystal symmetry operation12_565x,x-y+1,-z+1/21
Buried area23590 Å2
ΔGint-264 kcal/mol
Surface area55570 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)144.713, 144.713, 83.166
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Ribonuclease PH / RNase PH


Mass: 28322.338 Da / Num. of mol.: 1 / Mutation: R126A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / References: UniProt: O67069, tRNA nucleotidyltransferase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 4.44 Å3/Da / Density % sol: 72.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: ammonium sulfate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris-HCl1droppH8.0
25 mM1dropMgCl2
350 mM1dropKCl
410 mM1dropNaH2PO4
51.5 mg/mlprotein1drop
62 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 6, 2003 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 23220 / Num. obs: 22895 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 26.2
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.317 / % possible all: 98.3
Reflection
*PLUS
Redundancy: 13.2 %
Reflection shell
*PLUS
% possible obs: 98.3 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→41.78 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2266291.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 2269 9.9 %RANDOM
Rwork0.221 ---
obs0.221 22838 98.3 %-
all-23233 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.8374 Å2 / ksol: 0.345658 e/Å3
Displacement parametersBiso mean: 52.5 Å2
Baniso -1Baniso -2Baniso -3
1--7.18 Å22.01 Å20 Å2
2---7.18 Å20 Å2
3---14.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.3→41.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1975 0 15 95 2085
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.151.5
X-RAY DIFFRACTIONc_mcangle_it4.492
X-RAY DIFFRACTIONc_scbond_it4.192
X-RAY DIFFRACTIONc_scangle_it6.112.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.348 366 10.1 %
Rwork0.336 3255 -
obs--95.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 50 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86

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