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- PDB-5y9a: Crystal structure of the complex of peptidyl tRNA hydrolase with ... -

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Basic information

Entry
Database: PDB / ID: 5y9a
TitleCrystal structure of the complex of peptidyl tRNA hydrolase with a phosphate ion at the substrate binding site and cytarabine at a new ligand binding site at 1.1 A resolution
ComponentsPeptidyl-tRNA hydrolase
KeywordsHYDROLASE
Function / homology
Function and homology information


peptidyl-tRNA hydrolase / peptidyl-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
CYTARABINE / PHOSPHATE ION / Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsKaushik, S. / Iqbal, N. / Singh, N. / 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: 4LWR
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)21,5883
Polymers21,2501
Non-polymers3382
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-7 kcal/mol
Surface area8930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.000, 66.160, 76.150
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: 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-AR3 / CYTARABINE / 1-BETA-D-ARABINOFURANOSYLCYTOSINE / ARA-C


Mass: 243.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N3O5 / Comment: medication, chemotherapy*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.02 Å3/Da / Density % sol: 38.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 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: 1.1→16.85 Å / Num. obs: 68259 / % possible obs: 96.9 % / Redundancy: 3.8 % / Net I/σ(I): 13.3
Reflection shellResolution: 1.1→1.16 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: 4LWR

4lwr
PDB Unreleased entry


Resolution: 1.1→16.85 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.846 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.03 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1593 3454 5.1 %RANDOM
Rwork0.12543 ---
obs0.12712 64713 96.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.136 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0 Å2-0 Å2
2---0.09 Å20 Å2
3---0.25 Å2
Refinement stepCycle: 1 / Resolution: 1.1→16.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1496 0 22 245 1763
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0191554
X-RAY DIFFRACTIONr_bond_other_d00.021489
X-RAY DIFFRACTIONr_angle_refined_deg2.1661.9662102
X-RAY DIFFRACTIONr_angle_other_deg3.27233423
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9235195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.34823.91369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.87115254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.626159
X-RAY DIFFRACTIONr_chiral_restr0.170.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211787
X-RAY DIFFRACTIONr_gen_planes_other0.020.02371
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_it2.5871.047783
X-RAY DIFFRACTIONr_mcbond_other2.5891.045782
X-RAY DIFFRACTIONr_mcangle_it2.9951.585977
X-RAY DIFFRACTIONr_mcangle_other2.9991.586978
X-RAY DIFFRACTIONr_scbond_it3.3911.462771
X-RAY DIFFRACTIONr_scbond_other3.3941.462767
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.962.0341120
X-RAY DIFFRACTIONr_long_range_B_refined5.99611.6761910
X-RAY DIFFRACTIONr_long_range_B_other5.03210.1131778
X-RAY DIFFRACTIONr_rigid_bond_restr10.74833043
X-RAY DIFFRACTIONr_sphericity_free48.807554
X-RAY DIFFRACTIONr_sphericity_bonded12.62953198
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 263 -
Rwork0.236 4617 -
obs--94.9 %

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