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- PDB-4z86: Crystal structure of Peptidyl-tRNA hydrolase mutant -N118D from V... -

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Basic information

Entry
Database: PDB / ID: 4z86
TitleCrystal structure of Peptidyl-tRNA hydrolase mutant -N118D from Vibrio cholerae at 1.63A resolution.
ComponentsPeptidyl-tRNA hydrolase
KeywordsHYDROLASE / Peptidyl tRNA hydrolase / N118D mutant Vibrio cholerae Hydrolase
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
Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.63 Å
AuthorsShahid, S. / Kabra, A. / Pal, R.K. / Arora, A.
CitationJournal: RNA / Year: 2017
Title: Unraveling the stereochemical and dynamic aspects of the catalytic site of bacterial peptidyl-tRNA hydrolase.
Authors: Kabra, A. / Shahid, S. / Pal, R.K. / Yadav, R. / Pulavarti, S.V. / Jain, A. / Tripathi, S. / Arora, A.
History
DepositionApr 8, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
B: Peptidyl-tRNA hydrolase


Theoretical massNumber of molelcules
Total (without water)43,5542
Polymers43,5542
Non-polymers00
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-14 kcal/mol
Surface area16300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.112, 71.124, 124.030
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: 21777.150 Da / Num. of mol.: 2 / Mutation: N118D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: pth, VC_2184 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KQ21, peptidyl-tRNA hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.25 Å3/Da / Density % sol: 45.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100mM Soduim citrate, 200mM Ammonium acetate, 25% Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.63→62.01 Å / Num. obs: 49251 / % possible obs: 98.9 % / Redundancy: 6.1 % / Net I/σ(I): 51.92
Reflection shellResolution: 1.63→1.69 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 4.68 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing
RefinementResolution: 1.63→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.659 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2069 2483 5 %RANDOM
Rwork0.17019 ---
obs0.17201 46686 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.187 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å2-0 Å2-0 Å2
2--1.21 Å2-0 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 1.63→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3008 0 0 289 3297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0193068
X-RAY DIFFRACTIONr_bond_other_d0.0020.023033
X-RAY DIFFRACTIONr_angle_refined_deg2.081.9764141
X-RAY DIFFRACTIONr_angle_other_deg0.92236981
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4075390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.46124.504131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.29415538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5571516
X-RAY DIFFRACTIONr_chiral_restr0.1240.2460
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213472
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02676
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_it2.432.311566
X-RAY DIFFRACTIONr_mcbond_other2.4292.3081565
X-RAY DIFFRACTIONr_mcangle_it3.4193.4531954
X-RAY DIFFRACTIONr_mcangle_other3.4193.4561955
X-RAY DIFFRACTIONr_scbond_it3.7592.7291502
X-RAY DIFFRACTIONr_scbond_other3.7572.7311503
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4683.9232187
X-RAY DIFFRACTIONr_long_range_B_refined6.80119.9663633
X-RAY DIFFRACTIONr_long_range_B_other6.7219.4483508
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.629→1.671 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 188 -
Rwork0.291 3263 -
obs--95.28 %

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