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- PDB-3td2: Crystal structures of Peptidyl-tRNA hydrolase from Mycobacterium ... -

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Basic information

Entry
Database: PDB / ID: 3td2
TitleCrystal structures of Peptidyl-tRNA hydrolase from Mycobacterium tuberculosis - Form 5
ComponentsPeptidyl-tRNA hydrolaseAlternative ribosome-rescue factor B
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: 2.5 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 10, 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
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.310, 60.310, 87.670
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Peptidyl-tRNA hydrolase / Alternative ribosome-rescue factor B / 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 / Water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.25 Å3/Da / Density % sol: 45.25 %
Crystal growTemperature: 291 K / Method: microbatch under oil / pH: 7.5
Details: 0.1M HEPES, 25% PEG 8000, 5% dioxane, 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: Jun 8, 2010
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 6725 / % possible obs: 99.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 72.9 Å2 / Rmerge(I) obs: 0.081
Reflection shellResolution: 2.5→2.64 Å

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z2I

2z2i


Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.946 / SU B: 26.989 / SU ML: 0.309 / Cross valid method: THROUGHOUT / ESU R Free: 0.308 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25541 320 4.8 %RANDOM
Rwork0.23655 ---
obs0.23747 6392 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 62.471 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å2-0.72 Å20 Å2
2---1.45 Å20 Å2
3---2.17 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1363 0 0 72 1435
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221387
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.9751878
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9835186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.11922.85756
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.92515217
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3251513
X-RAY DIFFRACTIONr_chiral_restr0.0970.2212
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021066
X-RAY DIFFRACTIONr_nbd_refined0.2360.2630
X-RAY DIFFRACTIONr_nbtor_refined0.3150.2924
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.256
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2730.28
X-RAY DIFFRACTIONr_mcbond_it0.9821.5939
X-RAY DIFFRACTIONr_mcangle_it1.68121454
X-RAY DIFFRACTIONr_scbond_it1.5533481
X-RAY DIFFRACTIONr_scangle_it2.384.5424
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 23 -
Rwork0.344 466 -
obs--99.39 %
Refinement TLS params.Method: refined / Origin x: 15.9793 Å / Origin y: -20.6115 Å / Origin z: 10.5145 Å
111213212223313233
T0.0516 Å2-0.0274 Å2-0.0488 Å2-0.3833 Å20.033 Å2--0.21 Å2
L2.7695 °2-0.4083 °2-0.4757 °2-2.2864 °20.3005 °2--3.7242 °2
S-0.0507 Å °0.4603 Å °-0.1652 Å °-0.0885 Å °-0.1247 Å °0.0729 Å °-0.2111 Å °-0.031 Å °0.1754 Å °

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