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- PDB-3p2j: Crystal structure of peptidyl-tRNA hydrolase from Mycobacterium s... -

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Basic information

Entry
Database: PDB / ID: 3p2j
TitleCrystal structure of peptidyl-tRNA hydrolase from Mycobacterium smegmatis at 2.2 A resolution
ComponentsPeptidyl-tRNA hydrolase
KeywordsHYDROLASE
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 speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsKumar, A. / Singh, A. / Yadav, R. / Sinha, M. / Arora, A. / Sharma, S. / Singh, T.P.
CitationJournal: To be Published
Title: Crystal Structure of peptidyl-tRNA hydrolase from Mycobacterium smegmatis at 2.2 A resolution
Authors: Kumar, A. / Singh, A. / Yadav, R. / Sinha, M. / Arora, A. / Sharma, S. / Singh, T.P.
History
DepositionOct 2, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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)20,2701
Polymers20,2701
Non-polymers00
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.909, 58.943, 61.854
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: 20270.268 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / MC(2)155 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 De3 / References: UniProt: A0R3D3, peptidyl-tRNA hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHOR STATED THAT THERE WERE ERRORS IN THE SEQUENCE DATABASE, THE SEQUENCE IN THIS ENTRY ...AUTHOR STATED THAT THERE WERE ERRORS IN THE SEQUENCE DATABASE, THE SEQUENCE IN THIS ENTRY REPRESENTED THE CORRECT SEQUENCE.

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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: 2.02 Å3/Da / Density % sol: 39.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20mM Tris-HCl, 1mM EDTA, 50mM NaCl, 10% isopropanol, 30% PEG 1500, 5mM 2-mercaptoethanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.514 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 26, 2009 / Details: MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.514 Å / Relative weight: 1
ReflectionResolution: 2.22→42.67 Å / Num. all: 8170 / Num. obs: 8170 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 32.3 Å2 / Rsym value: 0.078 / Net I/σ(I): 11.9
Reflection shellResolution: 2.22→2.3 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.641 / % possible all: 89.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
AMoREphasing
REFMAC5.5.0109refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KJZ

3kjz


Resolution: 2.22→14.96 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.226 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21818 379 4.7 %RANDOM
Rwork0.1916 ---
all0.193 8170 --
obs0.19293 7744 95.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20 Å2
2---0.41 Å20 Å2
3----0.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.22→14.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1428 0 0 155 1583
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221455
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.9661972
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.6025190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.97922.88159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.98415237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7881513
X-RAY DIFFRACTIONr_chiral_restr0.110.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211104
X-RAY DIFFRACTIONr_mcbond_it1.2961.5943
X-RAY DIFFRACTIONr_mcangle_it2.32321510
X-RAY DIFFRACTIONr_scbond_it1.9733512
X-RAY DIFFRACTIONr_scangle_it3.1644.5462
LS refinement shellResolution: 2.224→2.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 20 -
Rwork0.333 514 -
obs--86.83 %

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