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- PDB-8x5t: Crystal structure of Thermus thermophilus peptidyl-tRNA hydrolase... -

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Basic information

Entry
Database: PDB / ID: 8x5t
TitleCrystal structure of Thermus thermophilus peptidyl-tRNA hydrolase in complex with adenosine 5'-monophosphate
ComponentsPeptidyl-tRNA hydrolase
KeywordsTRANSLATION / peptidyl-tRNA hydrolase
Function / homology
Function and homology information


peptidyl-tRNA hydrolase / peptidyl-tRNA hydrolase activity / tRNA binding / translation / cytoplasm
Similarity search - Function
Peptidyl-tRNA hydrolase signature 1. / Peptidyl-tRNA hydrolase / Peptidyl-tRNA hydrolase, conserved site / Peptidyl-tRNA hydrolase superfamily / Peptidyl-tRNA hydrolase
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / L(+)-TARTARIC ACID / Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsUehara, Y. / Matsumoto, A. / Nakazawa, T. / Fukuta, A. / Ando, K. / Oka, N. / Uchiumi, T. / Ito, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Binding mode between peptidyl-tRNA hydrolase and the peptidyl-A76 moiety of the substrate.
Authors: Uehara, Y. / Matsumoto, A. / Nakazawa, T. / Fukuta, A. / Ando, K. / Uchiumi, T. / Oka, N. / Ito, K.
History
DepositionNov 19, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-tRNA hydrolase
B: Peptidyl-tRNA hydrolase
C: Peptidyl-tRNA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,13310
Polymers61,8633
Non-polymers1,2717
Water10,737596
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.315, 120.315, 185.981
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-507-

HOH

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Components

#1: Protein Peptidyl-tRNA hydrolase / PTH


Mass: 20620.867 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: pth, TTHA1588 / Production host: Escherichia coli B (bacteria) / References: UniProt: Q5SHZ2, peptidyl-tRNA hydrolase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 596 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.17 Å3/Da / Density % sol: 61.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.9 M K/Na tartrate, 0.1 M MES buffer pH5.8, and 40 mM adenosine 5'-monophosphate

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→104.2 Å / Num. obs: 104619 / % possible obs: 99.9 % / Redundancy: 21.2 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 83.5
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 20.5 % / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 20.8 / Num. unique obs: 5177 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→104.2 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.921 / SU ML: 0.034 / Cross valid method: FREE R-VALUE / ESU R: 0.059 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16756 5230 5 %RANDOM
Rwork0.14415 ---
obs0.14533 99300 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.882 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.07 Å20 Å2
2--0.15 Å20 Å2
3----0.48 Å2
Refinement stepCycle: 1 / Resolution: 1.6→104.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4320 0 84 596 5000
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0194511
X-RAY DIFFRACTIONr_bond_other_d0.0030.024379
X-RAY DIFFRACTIONr_angle_refined_deg2.9082.0076104
X-RAY DIFFRACTIONr_angle_other_deg1.276310031
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8225551
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.43321.045201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76615725
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8371560
X-RAY DIFFRACTIONr_chiral_restr0.1690.2647
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0215042
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021076
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1641.6272213
X-RAY DIFFRACTIONr_mcbond_other2.1521.6262212
X-RAY DIFFRACTIONr_mcangle_it2.8922.4362761
X-RAY DIFFRACTIONr_mcangle_other2.8912.4372762
X-RAY DIFFRACTIONr_scbond_it3.8192.0552298
X-RAY DIFFRACTIONr_scbond_other3.8182.0542298
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5162.9213344
X-RAY DIFFRACTIONr_long_range_B_refined6.9914.9785488
X-RAY DIFFRACTIONr_long_range_B_other6.80414.1125179
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.177 402 -
Rwork0.146 7226 -
obs--99.96 %

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