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- PDB-4jwk: Crystal structure of the complex of peptidyl-tRNA hydrolase from ... -

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Basic information

Entry
Database: PDB / ID: 4jwk
TitleCrystal structure of the complex of peptidyl-tRNA hydrolase from Acinetobacter baumannii with cytidine at 1.87 A resolution
ComponentsPeptidyl-tRNA hydrolase
KeywordsHYDROLASE / Protein synthesis / complex
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 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
4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesAcinetobacter baumannii ATCC 19606 = CIP 70.34 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsKaushik, S. / Singh, N. / Yamini, S. / Singh, A. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: Plos One / Year: 2013
Title: The Mode of Inhibitor Binding to Peptidyl-tRNA Hydrolase: Binding Studies and Structure Determination of Unbound and Bound Peptidyl-tRNA Hydrolase from Acinetobacter baumannii
Authors: Kaushik, S. / Singh, N. / Yamini, S. / Singh, A. / Sinha, M. / Arora, A. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionMar 27, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Aug 14, 2013Group: Database references
Revision 1.3Nov 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

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Assembly

Deposited unit
A: Peptidyl-tRNA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2112
Polymers20,9681
Non-polymers2431
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.257, 64.391, 78.612
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: 20967.957 Da / Num. of mol.: 1 / Fragment: Peptidyl-tRNA hydrolase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii ATCC 19606 = CIP 70.34 (bacteria)
Gene: HMPREF0010_01329, pth / Production host: Escherichia coli (E. coli) / References: UniProt: D0C9L6, peptidyl-tRNA hydrolase
#2: Chemical ChemComp-CTN / 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / CYTIDINE


Mass: 243.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N3O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.07 Å3/Da / Density % sol: 40.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M HEPES, 25% PEG400, 12% PEG1500, pH 6.5, 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 20, 2012
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.87→33.57 Å / Num. all: 14968 / Num. obs: 14269 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.87→1.9 Å / % possible all: 100

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Processing

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

4iko


Resolution: 1.87→33.57 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.714 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22156 756 5 %RANDOM
Rwork0.17867 ---
obs0.18072 14269 99.66 %-
all-14968 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.862 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å2-0 Å2-0 Å2
2--0.13 Å2-0 Å2
3---1.08 Å2
Refinement stepCycle: LAST / Resolution: 1.87→33.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1476 0 17 136 1629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191529
X-RAY DIFFRACTIONr_bond_other_d0.0020.021474
X-RAY DIFFRACTIONr_angle_refined_deg1.1131.9662068
X-RAY DIFFRACTIONr_angle_other_deg0.73433388
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2145192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.42723.97168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54515252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.204159
X-RAY DIFFRACTIONr_chiral_restr0.0620.2220
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211760
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02364
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.87→1.915 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 53 -
Rwork0.213 1011 -
obs--95.94 %

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