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- PDB-8x5u: Crystal structure of Thermus thermophilus peptidyl-tRNA hydrolase... -

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Basic information

Entry
Database: PDB / ID: 8x5u
TitleCrystal structure of Thermus thermophilus peptidyl-tRNA hydrolase C-terminal 16 amino acid deletion mutant
ComponentsPeptidyl-tRNA hydrolase
KeywordsTRANSLATION / peptidyl-tRNA hydrolase
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 signature 1. / Peptidyl-tRNA hydrolase / Peptidyl-tRNA hydrolase, conserved site / Peptidyl-tRNA hydrolase superfamily / Peptidyl-tRNA hydrolase
Similarity search - Domain/homology
Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6808
Polymers19,0081
Non-polymers6727
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-20 kcal/mol
Surface area8380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.948, 81.948, 123.940
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-206-

SO4

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Components

#1: Protein Peptidyl-tRNA hydrolase


Mass: 19007.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: pth / Production host: Escherichia coli B (bacteria) / References: UniProt: Q5SHZ2
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 3.21 Å3/Da / Density % sol: 61.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.5 M (NH4)2SO4, 0.1 M Tris-HCl pH7.5, 30% (v/v) PEG600, and 10% (v/v) glycerol

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→70.97 Å / Num. obs: 15036 / % possible obs: 100 % / Redundancy: 18.8 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 40.2
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 18 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 7.5 / Num. unique obs: 716 / % 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: 2.1→70.97 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.95 / SU ML: 0.108 / Cross valid method: FREE R-VALUE / ESU R: 0.175 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24792 768 5.1 %RANDOM
Rwork0.20127 ---
obs0.20361 14220 99.95 %-
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: 39.971 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20.14 Å20 Å2
2--0.28 Å20 Å2
3----0.91 Å2
Refinement stepCycle: 1 / Resolution: 2.1→70.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1320 0 35 60 1415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191379
X-RAY DIFFRACTIONr_bond_other_d0.0020.021331
X-RAY DIFFRACTIONr_angle_refined_deg2.0092.0111868
X-RAY DIFFRACTIONr_angle_other_deg1.10233044
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3745167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.65420.96862
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.65415225
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0771519
X-RAY DIFFRACTIONr_chiral_restr0.1270.2200
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211524
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02325
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_it3.9773.607671
X-RAY DIFFRACTIONr_mcbond_other3.9773.607670
X-RAY DIFFRACTIONr_mcangle_it55.385837
X-RAY DIFFRACTIONr_mcangle_other4.9975.385838
X-RAY DIFFRACTIONr_scbond_it5.2844.26707
X-RAY DIFFRACTIONr_scbond_other5.1424.15679
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4586.013988
X-RAY DIFFRACTIONr_long_range_B_refined10.2729.7991515
X-RAY DIFFRACTIONr_long_range_B_other10.05329.6111501
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å
RfactorNum. reflection% reflection
Rfree0.379 49 -
Rwork0.19 1026 -
obs--99.63 %

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