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- PDB-2z2j: Crystal structure of Peptidyl-tRNA hydrolase from Mycobacterium t... -

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Basic information

Entry
Database: PDB / ID: 2z2j
TitleCrystal structure of Peptidyl-tRNA hydrolase from Mycobacterium tuberculosis
ComponentsPeptidyl-tRNA hydrolase
KeywordsHYDROLASE / Protein synthesis
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: 2.35 Å
AuthorsSelvaraj, M. / Roy, S. / Singh, N.S. / Sangeetha, R. / Varshney, U. / Vijayan, M.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural Plasticity and Enzyme Action: Crystal Structures of Mycobacterium tuberculosis Peptidyl-tRNA Hydrolase
Authors: Selvaraj, M. / Roy, S. / Singh, N.S. / Sangeetha, R. / Varshney, U. / Vijayan, M.
History
DepositionMay 22, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 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
B: Peptidyl-tRNA hydrolase


Theoretical massNumber of molelcules
Total (without water)40,9712
Polymers40,9712
Non-polymers00
Water5,729318
1
A: Peptidyl-tRNA hydrolase


Theoretical massNumber of molelcules
Total (without water)20,4861
Polymers20,4861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidyl-tRNA hydrolase


Theoretical massNumber of molelcules
Total (without water)20,4861
Polymers20,4861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.823, 73.763, 59.791
Angle α, β, γ (deg.)90.00, 92.35, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a monomer

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Components

#1: Protein Peptidyl-tRNA hydrolase / PTH


Mass: 20485.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv1014c, pth / Plasmid: pRSETBMtuPth / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: P65865, UniProt: P9WHN7*PLUS, peptidyl-tRNA hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 1.93 Å3/Da / Density % sol: 36.12 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 6.6
Details: 25%(w/v) PEG 8000, 100mm Na cacodylate, 5%(v/v) 2-propanol, pH 6.6, Microbatch, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 15, 2006
RadiationMonochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 12613 / % possible obs: 96.8 % / Redundancy: 2.9 % / Biso Wilson estimate: 21.3 Å2 / Rsym value: 0.118 / Net I/σ(I): 9.05
Reflection shellResolution: 2.35→2.43 Å / Mean I/σ(I) obs: 2.7 / Num. unique all: 1236 / Rsym value: 0.411 / % possible all: 95.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PTH

2pth


Resolution: 2.35→22.49 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1035292.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 647 5.1 %RANDOM
Rwork0.196 ---
obs0.196 12613 96.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.0269 Å2 / ksol: 0.328534 e/Å3
Displacement parametersBiso mean: 23.7 Å2
Baniso -1Baniso -2Baniso -3
1--5.18 Å20 Å21.37 Å2
2---2.48 Å20 Å2
3---7.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.35→22.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2699 0 0 318 3017
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_mcbond_it1.011.5
X-RAY DIFFRACTIONc_mcangle_it1.572
X-RAY DIFFRACTIONc_scbond_it1.732
X-RAY DIFFRACTIONc_scangle_it2.492.5
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.341 108 5.2 %
Rwork0.258 1951 -
obs-1951 94.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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