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- PDB-3kk0: Crystal structure of partially folded intermediate state of pepti... -

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Basic information

Entry
Database: PDB / ID: 3kk0
TitleCrystal structure of partially folded intermediate state of peptidyl-tRNA hydrolase from Mycobacterium smegmatis
ComponentsPeptidyl-tRNA hydrolase
KeywordsHYDROLASE / Protein synthesis
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
BETA-MERCAPTOETHANOL / ISOPROPYL ALCOHOL / DI(HYDROXYETHYL)ETHER / Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsKumar, A. / Singh, N. / Yadav, R. / Sharma, S. / Arora, A. / Singh, T.P.
CitationJournal: To be Published
Title: Structures of Fully-Folded Native and Partially-Folded Intermediate States of Peptidyl-tRNA Hydrolase from Mycobacterium smegmatis
Authors: Kumar, A. / Singh, N. / Yadav, R. / Sharma, S. / Arora, A. / Singh, T.P.
History
DepositionNov 4, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidyl-tRNA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,88310
Polymers20,2701
Non-polymers6139
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.006, 65.597, 68.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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 str. MC2 155 (bacteria)
Strain: ATCC 700084 / mc(2)155 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: A0R3D3, peptidyl-tRNA hydrolase

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Non-polymers , 5 types, 179 molecules

#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHERE ARE CONFLICTS BETWEEN THE REPORTED SEQUENCE AND DATABASE REFERENCE SEQUENCE. THE DEPOSITORS ...THERE ARE CONFLICTS BETWEEN THE REPORTED SEQUENCE AND DATABASE REFERENCE SEQUENCE. THE DEPOSITORS BUILT THESE RESIDUES ON THE BASIS OF THE OBSERVED ELECTRON DENSITY.

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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: 2.78 Å3/Da / Density % sol: 55.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20mM Tris-HCl, 1mM EDTA, 50mM NaCl, 5mM 2-mercaptoethanol, 5% (w/v) PEG 400, 10% isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 13, 2009 / Details: Mirror
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.65→25.99 Å / Num. all: 6932 / Num. obs: 6733 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 52.1 Å2
Reflection shellResolution: 2.65→2.7 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KJZ

3kjz


Resolution: 2.65→25.99 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 79196.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 376 5.6 %RANDOM
Rwork0.223 ---
all0.24 6932 --
obs0.237 6733 97.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 148.192 Å2 / ksol: 0.241404 e/Å3
Displacement parametersBiso mean: 37.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å20 Å2
2---0.67 Å20 Å2
3---0.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.65→25.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1427 0 39 170 1636
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.64
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.31.5
X-RAY DIFFRACTIONc_mcangle_it3.72
X-RAY DIFFRACTIONc_scbond_it2.742
X-RAY DIFFRACTIONc_scangle_it3.862.5
LS refinement shellResolution: 2.65→2.82 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3917 67 6.1 %
Rwork0.3306 1038 -
obs--99.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION5ioh.paramioh.top

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