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- PDB-3vjr: Crystal structure of Peptidyl-tRNA hydrolase from Escherichia col... -

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Basic information

Entry
Database: PDB / ID: 3vjr
TitleCrystal structure of Peptidyl-tRNA hydrolase from Escherichia coli in complex with the CCA-acceptor-T[PSI]C domain of tRNA
Components
  • Peptidyl-tRNA hydrolase
  • tRNA CCA-acceptor
Keywordshydrolase/RNA / Peptidyl-tRNA hydrolase / CCA-acceptor-T[PSI]C domain / seven beta-strands form / hydrolase-RNA complex
Function / homology
Function and homology information


peptidyl-tRNA hydrolase / peptidyl-tRNA hydrolase activity / protein quality control for misfolded or incompletely synthesized proteins / rescue of stalled ribosome / tRNA binding / cytoplasm
Similarity search - Function
Peptidyl-tRNA hydrolase / Peptidyl-tRNA hydrolase signature 2. / Peptidyl-tRNA hydrolase signature 1. / Peptidyl-tRNA hydrolase / Peptidyl-tRNA hydrolase, conserved site / Peptidyl-tRNA hydrolase superfamily / Peptidyl-tRNA hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsIto, K. / Murakami, R. / Mochizuki, M. / Qi, H. / Shimizu, Y. / Miura, K.I. / Ueda, T. / Uchiumi, T.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Structural basis for the substrate recognition and catalysis of peptidyl-tRNA hydrolase.
Authors: Ito, K. / Murakami, R. / Mochizuki, M. / Qi, H. / Shimizu, Y. / Miura, K. / Ueda, T. / Uchiumi, T.
History
DepositionOct 28, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidyl-tRNA hydrolase
B: tRNA CCA-acceptor
C: Peptidyl-tRNA hydrolase
D: tRNA CCA-acceptor


Theoretical massNumber of molelcules
Total (without water)65,8574
Polymers65,8574
Non-polymers00
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-40 kcal/mol
Surface area27680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.070, 55.070, 413.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Peptidyl-tRNA hydrolase / PTH


Mass: 21395.588 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: pth, b1204, JW1195 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7D1, peptidyl-tRNA hydrolase
#2: RNA chain tRNA CCA-acceptor


Mass: 11532.882 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA WAS REPEATED BY IN VITRO TRANSCRIPTION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.75 Å3/Da / Density % sol: 55.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 100mM acetate buffer, 20% (w/v) 1,4-butanediol, 30mM glycyl-glycyl-glycine , pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 22, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 27129 / Num. obs: 27129 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Rmerge(I) obs: 0.056 / Rsym value: 0.059 / Net I/σ(I): 24.94
Reflection shellResolution: 2.4→2.54 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 8.2 / Num. unique all: 4136 / Rsym value: 0.2 / % possible all: 93.7

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Processing

Software
NameVersionClassification
XDSdata scaling
MOLREPphasing
REFMAC5.5.0109refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PTH

2pth


Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / SU B: 15.482 / SU ML: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23657 1390 5 %RANDOM
Rwork0.19251 ---
all0.19472 26216 --
obs0.19472 26216 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 47.222 Å2
Baniso -1Baniso -2Baniso -3
1-3.14 Å21.57 Å20 Å2
2--3.14 Å20 Å2
3----4.72 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2960 1532 0 139 4631
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0214734
X-RAY DIFFRACTIONr_angle_refined_deg1.3662.3716752
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4035384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.9423.333132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.815504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2571522
X-RAY DIFFRACTIONr_chiral_restr0.0770.2810
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213046
X-RAY DIFFRACTIONr_mcbond_it0.4881.51908
X-RAY DIFFRACTIONr_mcangle_it0.93623042
X-RAY DIFFRACTIONr_scbond_it1.332826
X-RAY DIFFRACTIONr_scangle_it2.0254.53710
LS refinement shellResolution: 2.399→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 103 -
Rwork0.258 1865 -
obs-1968 99.14 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.51360.0314-0.13762.1424-0.05232.337-0.1280.0327-0.0498-0.05-0.03280.10250.19580.06410.16080.1583-0.08430.03310.0651-0.02930.1091-22.07679.79091.8265
20.57980.06070.26170.49111.03662.77150.03020.03820.1209-0.0403-0.0637-0.0696-0.2018-0.21910.03350.1711-0.0706-0.03070.1066-0.00340.1483-18.224932.5519-3.273
32.0477-0.1790.2291.74530.09512.2009-0.0381-0.0871-0.0674-0.0041-0.12070.1046-0.1642-0.13660.15880.0214-0.0020.01810.2131-0.04420.1143-30.116423.6566-40.8329
40.560.1822-1.02960.2889-0.25842.4748-0.06760.00380.01790.05410.0151-0.14170.33930.04770.05250.1107-0.00430.01310.22620.01210.1663-8.346415.581-35.8746
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 197
2X-RAY DIFFRACTION2B1 - 36
3X-RAY DIFFRACTION3C5 - 197
4X-RAY DIFFRACTION4D1 - 36

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