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- PDB-7wt6: Crystal structure of full-length peptidyl-tRNA hydrolase from Myc... -

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Basic information

Entry
Database: PDB / ID: 7wt6
TitleCrystal structure of full-length peptidyl-tRNA hydrolase from Mycobacterium tuberculosis
ComponentsPeptidyl-tRNA hydrolase
KeywordsHYDROLASE / Enzyme classification / Peptidyl-tRNA
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 / plasma membrane / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesMycobacteriaceae bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsKulandaisamy, R. / Das, U. / Inampudi, K.K.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)EEQ/2016/000507 India
Department of Biotechnology (DBT, India)BT/PR34319/Med/29/1488/2019 India
CitationJournal: To Be Published
Title: Crystal structure of full-length peptidyl-tRNA hydrolase from Mycobacterium tuberculosis
Authors: Kulandaisamy, R. / Das, U. / Inampudi, K.K.
History
DepositionFeb 4, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-tRNA hydrolase


Theoretical massNumber of molelcules
Total (without water)21,8041
Polymers21,8041
Non-polymers00
Water3,927218
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9050 Å2
Unit cell
Length a, b, c (Å)36.581, 39.003, 123.818
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Peptidyl-tRNA hydrolase / PTH


Mass: 21803.990 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacteriaceae bacterium (bacteria) / Strain: H37Rv / Gene: pth / Production host: Escherichia coli (E. coli) / References: UniProt: P9WHN7, peptidyl-tRNA hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal growTemperature: 293.15 K / Method: microbatch
Details: 25% (W/V) PEG 8000, 0.1M HEPES pH 7.5 5% (V/V) 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976254 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 26, 2021 / Details: Vertical CRL/ Horizontal Eliptical mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 1.937→37.201 Å / Num. obs: 13646 / % possible obs: 98.61 % / Redundancy: 8 % / Biso Wilson estimate: 18.92 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.055 / Rrim(I) all: 0.159 / Net I/σ(I): 11.4
Reflection shellResolution: 1.937→1.97 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 587 / CC1/2: 0.887 / Rpim(I) all: 0.29 / Rrim(I) all: 0.78 / % possible all: 87.7

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z2I

2z2i


Resolution: 1.94→37.2 Å / SU ML: 0.2299 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.7634 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2145 729 5.34 %
Rwork0.1687 12915 -
obs0.1712 13638 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.58 Å2
Refinement stepCycle: LAST / Resolution: 1.94→37.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1427 0 0 218 1645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00581454
X-RAY DIFFRACTIONf_angle_d0.79311965
X-RAY DIFFRACTIONf_chiral_restr0.0506215
X-RAY DIFFRACTIONf_plane_restr0.0057264
X-RAY DIFFRACTIONf_dihedral_angle_d6.7057878
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-2.090.25181360.19182396X-RAY DIFFRACTION94.41
2.09-2.30.23911560.17712570X-RAY DIFFRACTION99.49
2.3-2.630.24261310.17182586X-RAY DIFFRACTION99.67
2.63-3.310.22461540.17252625X-RAY DIFFRACTION99.89
3.31-37.20.18181520.15682738X-RAY DIFFRACTION99.48

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