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- PDB-5y98: Crystal structure of native unbound peptidyl tRNA hydrolase from ... -

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Basic information

Entry
Database: PDB / ID: 5y98
TitleCrystal structure of native unbound peptidyl tRNA hydrolase from Acinetobacter baumannii at 1.36 A resolution
ComponentsPeptidyl-tRNA hydrolaseAlternative ribosome-rescue factor B
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
Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsIqbal, N. / Singh, N. / Kaushik, S. / Singh, P.K. / Sharma, S. / Singh, T.P.
CitationJournal: Biochem. J. / Year: 2018
Title: Search of multiple hot spots on the surface of peptidyl-tRNA hydrolase: structural, binding and antibacterial studies.
Authors: Kaushik, S. / Iqbal, N. / Singh, N. / Sikarwar, J.S. / Singh, P.K. / Sharma, P. / Kaur, P. / Sharma, S. / Owais, M. / Singh, T.P.
History
DepositionAug 23, 2017Deposition site: PDBJ / Processing site: PDBJ
SupersessionSep 13, 2017ID: 3WH4
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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

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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)21,3422
Polymers21,2501
Non-polymers921
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-1 kcal/mol
Surface area8940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.980, 65.970, 75.880
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 / Alternative ribosome-rescue factor B / PTH


Mass: 21250.232 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81) (bacteria)
Strain: ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81
Gene: pth, F911_03144, HMPREF0010_01329 / Production host: Escherichia coli (E. coli) / References: UniProt: D0C9L6, peptidyl-tRNA hydrolase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 216 / 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 Å3/Da / Density % sol: 38.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50mM HEPES, PEG 400, PEG 1500, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 23, 2013 / Details: Mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.36→25.32 Å / Num. obs: 37477 / % possible obs: 99.9 % / Redundancy: 4.2 % / Net I/σ(I): 20.2
Reflection shellResolution: 1.36→1.395 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WH4

3wh4
PDB Unreleased entry


Resolution: 1.36→25.32 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.354 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.044 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14449 1871 5 %RANDOM
Rwork0.10621 ---
obs0.10807 35544 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.678 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0 Å2
2---0.02 Å20 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.36→25.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1496 0 6 216 1718
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0191543
X-RAY DIFFRACTIONr_bond_other_d0.0020.021489
X-RAY DIFFRACTIONr_angle_refined_deg2.211.9512083
X-RAY DIFFRACTIONr_angle_other_deg2.79933423
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.79324.08571
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88215256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.868159
X-RAY DIFFRACTIONr_chiral_restr0.1570.2219
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211788
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02369
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_it3.961.086783
X-RAY DIFFRACTIONr_mcbond_other3.9641.083782
X-RAY DIFFRACTIONr_mcangle_it5.4971.638977
X-RAY DIFFRACTIONr_mcangle_other5.4951.639978
X-RAY DIFFRACTIONr_scbond_it4.2881.447760
X-RAY DIFFRACTIONr_scbond_other4.2891.448760
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0492.0211107
X-RAY DIFFRACTIONr_long_range_B_refined7.27911.1241879
X-RAY DIFFRACTIONr_long_range_B_other7.06910.1481778
X-RAY DIFFRACTIONr_rigid_bond_restr9.09733032
X-RAY DIFFRACTIONr_sphericity_free39.582545
X-RAY DIFFRACTIONr_sphericity_bonded13.73153168
LS refinement shellResolution: 1.36→1.395 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 140 -
Rwork0.164 2561 -
obs--99.26 %

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