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- PDB-4jx9: Crystal structure of the complex of peptidyl t-RNA hydrolase from... -

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Basic information

Entry
Database: PDB / ID: 4jx9
TitleCrystal structure of the complex of peptidyl t-RNA hydrolase from Acinetobacter baumannii with uridine at 1.4A 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
URIDINE / Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesAcinetobacter baumannii ATCC 19606 = CIP 70.34 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 28, 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)21,2122
Polymers20,9681
Non-polymers2441
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.945, 65.783, 75.752
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: pth, HMPREF0010_01329 / Production host: Escherichia coli (E. coli) / References: UniProt: D0C9L6, peptidyl-tRNA hydrolase
#2: Chemical ChemComp-URI / URIDINE


Mass: 244.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12N2O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 39.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M HEPES, 25% PEG400, 30% 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: 1.4→28.04 Å / Num. all: 32452 / Num. obs: 32452 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.4→1.43 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: 1.4→28.04 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.945 / SU B: 0.944 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.071 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20908 1731 5.1 %RANDOM
Rwork0.19257 ---
obs0.1934 32452 99.85 %-
all-32452 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.554 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0 Å20 Å2
2--0.23 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.4→28.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1476 0 17 217 1710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0191529
X-RAY DIFFRACTIONr_bond_other_d0.0010.021473
X-RAY DIFFRACTIONr_angle_refined_deg1.1181.9662068
X-RAY DIFFRACTIONr_angle_other_deg0.71133387
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2275192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.87423.97168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.07815252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.975159
X-RAY DIFFRACTIONr_chiral_restr0.0580.2220
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211758
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02361
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: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 105 -
Rwork0.214 2332 -
obs--98.7 %

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