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- PDB-4qd3: Crystal structure of Peptidyl-tRNA hydrolase from Pseudomonas aer... -

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Basic information

Entry
Database: PDB / ID: 4qd3
TitleCrystal structure of Peptidyl-tRNA hydrolase from Pseudomonas aeruginosa with 5-azacytidine at 1.89 Angstrom resolution
ComponentsPeptidyl-tRNA hydrolase
KeywordsHYDROLASE
Function / homology
Function and homology information


peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / translation / 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
Chem-5AE / Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsSingh, A. / Gautam, L. / Sinha, M. / Bhushan, A. / Kaur, P. / Sharma, S. / 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 13, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidyl-tRNA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1693
Polymers20,8331
Non-polymers3362
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.111, 64.111, 156.620
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: Chemical ChemComp-5AE / 4-amino-1-(beta-D-ribofuranosyl)-1,3,5-triazin-2(1H)-one / 5-azacytidine


Mass: 244.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H12N4O5 / Comment: medication*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.23 Å3/Da / Density % sol: 44.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, Isopropanol, 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: 1.89→32.08 Å / Num. all: 16071 / Num. obs: 16071 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.075 / Net I/σ(I): 51.7
Reflection shellResolution: 1.89→1.92 Å / Mean I/σ(I) obs: 4.5 / Rsym value: 0.491 / % possible all: 99.9

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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: 1.89→32.08 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.16 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23803 799 5 %RANDOM
Rwork0.18642 ---
obs0.18897 15212 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.774 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20.4 Å2-0 Å2
2--0.4 Å2-0 Å2
3----1.31 Å2
Refinement stepCycle: LAST / Resolution: 1.89→32.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1467 0 23 201 1691
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191521
X-RAY DIFFRACTIONr_bond_other_d00.021474
X-RAY DIFFRACTIONr_angle_refined_deg1.3051.9742056
X-RAY DIFFRACTIONr_angle_other_deg3.64833374
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8845193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.70323.0366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33215244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8171512
X-RAY DIFFRACTIONr_chiral_restr0.1090.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211746
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02366
X-RAY DIFFRACTIONr_mcbond_it1.2262.646775
X-RAY DIFFRACTIONr_mcbond_other1.2222.642774
X-RAY DIFFRACTIONr_mcangle_it2.0493.956967
X-RAY DIFFRACTIONr_mcangle_other2.053.961968
X-RAY DIFFRACTIONr_scbond_it1.552.929746
X-RAY DIFFRACTIONr_scbond_other1.5442.929746
X-RAY DIFFRACTIONr_scangle_other2.5774.2921090
X-RAY DIFFRACTIONr_long_range_B_refined5.5922.9081821
X-RAY DIFFRACTIONr_long_range_B_other5.58622.8971820
LS refinement shellResolution: 1.89→1.939 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 60 -
Rwork0.253 1094 -
obs--100 %

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