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- PDB-4qaj: Crystal structure of Peptidyl-tRNA hydrolase from Pseudomonas aer... -

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Basic information

Entry
Database: PDB / ID: 4qaj
TitleCrystal structure of Peptidyl-tRNA hydrolase from Pseudomonas aeruginosa at 1.5 Angstrom resolution
ComponentsPeptidyl-tRNA hydrolase
KeywordsHYDROLASE / Pth
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 cytosolic 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
Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSingh, A. / Kumar, A. / Gautam, L. / Sinha, M. / Bhushan, A. / Kaur, P. / Sharma, S. / Arora, A. / Singh, T.P.
CitationJournal: Biochem.J. / Year: 2014
Title: Structural and binding studies of peptidyl-tRNA hydrolase from Pseudomonas aeruginosa provide a platform for the structure-based inhibitor design against peptidyl-tRNA hydrolase
Authors: Singh, A. / Kumar, A. / Gautam, L. / Sharma, P. / Sinha, M. / Bhushan, A. / Kaur, P. / Sharma, S. / Arora, A. / Singh, T.P.
History
DepositionMay 5, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-tRNA hydrolase


Theoretical massNumber of molelcules
Total (without water)20,8331
Polymers20,8331
Non-polymers00
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.115, 64.115, 155.312
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Peptidyl-tRNA hydrolase / PTH


Mass: 20832.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA4672, pth / Plasmid: pEt28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(De3) / References: UniProt: Q9HVC3, peptidyl-tRNA hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, 5% isoproponal, 100mM HEPES buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 2, 2013 / Details: Mirror
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.5→29.64 Å / Num. all: 31169 / Num. obs: 31169 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Net I/σ(I): 50.3
Reflection shellResolution: 1.5→1.53 Å / Mean I/σ(I) obs: 2 / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JC4

4jc4


Resolution: 1.5→29.64 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.077 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22027 1571 5 %RANDOM
Rwork0.18004 ---
obs0.18206 29552 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.09 Å2-0 Å2
2--0.09 Å2-0 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1467 0 0 250 1717
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0191537
X-RAY DIFFRACTIONr_bond_other_d00.021506
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.9622087
X-RAY DIFFRACTIONr_angle_other_deg3.67433453
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6245203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.95923.04369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8515256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0411513
X-RAY DIFFRACTIONr_chiral_restr0.1270.2229
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211792
X-RAY DIFFRACTIONr_gen_planes_other0.0190.02373
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_it2.1662.14787
X-RAY DIFFRACTIONr_mcbond_other2.1412.135786
X-RAY DIFFRACTIONr_mcangle_it3.0473.199985
X-RAY DIFFRACTIONr_mcangle_other3.0573.204986
X-RAY DIFFRACTIONr_scbond_it3.0232.485750
X-RAY DIFFRACTIONr_scbond_other3.0172.484750
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.463.5811096
X-RAY DIFFRACTIONr_long_range_B_refined6.92419.7271895
X-RAY DIFFRACTIONr_long_range_B_other6.6218.4081769
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 113 -
Rwork0.273 2117 -
obs--99.29 %

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