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- PDB-3tck: Crystal structure of Peptidyl-tRNA hydrolase from Mycobacterium t... -

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Basic information

Entry
Database: PDB / ID: 3tck
TitleCrystal structure of Peptidyl-tRNA hydrolase from Mycobacterium tuberculosis - Form 4
ComponentsPeptidyl-tRNA hydrolase
KeywordsHYDROLASE / Pth / Hydrolysis of Peptidyl-tRNA / Peptidyl-tRNA / Cytosol
Function / homology
Function and homology information


peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / translation / plasma membrane / 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 / Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSelvaraj, M. / Ahmad, R. / Varshney, U. / Vijayan, M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Structures of new crystal forms of Mycobacterium tuberculosis peptidyl-tRNA hydrolase and functionally important plasticity of the molecule
Authors: Selvaraj, M. / Ahmad, R. / Varshney, U. / Vijayan, M.
History
DepositionAug 9, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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


Theoretical massNumber of molelcules
Total (without water)20,4861
Polymers20,4861
Non-polymers00
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.300, 38.810, 122.880
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: 20485.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT1042, MTCY10G2.35, pth, Rv1014c / Plasmid: PRSETBMtuPth / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P65865, UniProt: P9WHN7*PLUS, peptidyl-tRNA hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.11 Å3/Da / Density % sol: 41.78 %
Crystal growTemperature: 291 K / Method: microbatch under oil / pH: 7.5
Details: 0.1M HEPES, 15% PEG 8000, 5% isoproponal, pH 7.5, Microbatch under oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 3, 2010 / Details: mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 7780 / % possible obs: 95.4 % / Redundancy: 6.2 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.158 / Net I/σ(I): 11.4
Reflection shellResolution: 2.3→2.42 Å

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z2I

2z2i


Resolution: 2.3→30 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 412 5 %Random
Rwork0.2244 ---
obs-7780 --
Solvent computationBsol: 61.6401 Å2
Displacement parametersBiso mean: 20.395 Å2
Baniso -1Baniso -2Baniso -3
1-2.619 Å20 Å20 Å2
2---0.88 Å20 Å2
3----1.739 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1398 0 0 260 1658
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_refined_d0.008
X-RAY DIFFRACTIONc_angle_refined_deg1.8
X-RAY DIFFRACTIONc_mcbond_it1.3961.5
X-RAY DIFFRACTIONc_scbond_it1.8812
X-RAY DIFFRACTIONc_mcangle_it2.2192
X-RAY DIFFRACTIONc_scangle_it2.6772.5
LS refinement shellResolution: 2.3→2.42 Å
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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