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- PDB-5zx8: Crystal structure of peptidyl-tRNA hydrolase from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 5zx8
TitleCrystal structure of peptidyl-tRNA hydrolase from Thermus thermophilus
ComponentsPeptidyl-tRNA hydrolase
KeywordsHYDROLASE / peptidyl-tRNA hydrolase / Thermus thermophilus
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 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
CITRATE ANION / Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsMatsumoto, A. / Uehara, Y. / Shimizu, Y. / Ueda, T. / Uchiumi, T. / Ito, K.
CitationJournal: Proteins / Year: 2019
Title: High-resolution crystal structure of peptidyl-tRNA hydrolase from Thermus thermophilus.
Authors: Matsumoto, A. / Uehara, Y. / Shimizu, Y. / Ueda, T. / Uchiumi, T. / Ito, K.
History
DepositionMay 18, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 1.5Jun 4, 2025Group: Structure summary / Category: audit_author / Item: _audit_author.name

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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)21,2355
Polymers20,6211
Non-polymers6154
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-7 kcal/mol
Surface area9040 Å2
Unit cell
Length a, b, c (Å)47.453, 53.918, 58.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptidyl-tRNA hydrolase / PTH


Mass: 20620.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: pth, TTHA1588 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SHZ2, peptidyl-tRNA hydrolase
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
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: 1.82 Å3/Da / Density % sol: 32.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 100 mM phosphate-citrate buffer pH 4.2, 50%(v/v) 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1→50 Å / Num. obs: 75984 / % possible obs: 92.6 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 57.2
Reflection shellResolution: 1→1.04 Å / Rmerge(I) obs: 0.46

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RYB

1ryb


Resolution: 1→23.45 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.543 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.023 / ESU R Free: 0.022 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14272 3777 5 %RANDOM
Rwork0.12867 ---
obs0.12938 71946 92.25 %-
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: 16.198 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20 Å2
2--0.28 Å2-0 Å2
3---0.31 Å2
Refinement stepCycle: 1 / Resolution: 1→23.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1448 0 42 120 1610
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191554
X-RAY DIFFRACTIONr_bond_other_d0.0010.021536
X-RAY DIFFRACTIONr_angle_refined_deg1.8742.0172110
X-RAY DIFFRACTIONr_angle_other_deg0.9063.0013517
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2975195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.51420.88268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31115256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3861521
X-RAY DIFFRACTIONr_chiral_restr0.4290.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211740
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02365
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_it1.3511.264753
X-RAY DIFFRACTIONr_mcbond_other1.1791.26752
X-RAY DIFFRACTIONr_mcangle_it1.5561.908942
X-RAY DIFFRACTIONr_mcangle_other1.6011.911943
X-RAY DIFFRACTIONr_scbond_it3.9711.681801
X-RAY DIFFRACTIONr_scbond_other3.9691.682802
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0432.4011164
X-RAY DIFFRACTIONr_long_range_B_refined4.07911.7861789
X-RAY DIFFRACTIONr_long_range_B_other3.89911.4781753
X-RAY DIFFRACTIONr_rigid_bond_restr4.07433090
X-RAY DIFFRACTIONr_sphericity_free25.636529
X-RAY DIFFRACTIONr_sphericity_bonded10.50753144
LS refinement shellResolution: 0.999→1.025 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 263 -
Rwork0.221 5369 -
obs--94.07 %

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