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- PDB-4qt4: Crystal structure of Peptidyl-tRNA hydrolase from a Gram-positive... -

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Basic information

Entry
Database: PDB / ID: 4qt4
TitleCrystal structure of Peptidyl-tRNA hydrolase from a Gram-positive bacterium, Streptococcus pyogenes at 2.19 Angstrom resolution shows the Closed Structure of the Substrate Binding Cleft
ComponentsPeptidyl-tRNA hydrolase
KeywordsHYDROLASE / Pth / peptidyl-tRNA
Function / homology
Function and homology information


peptidyl-tRNA hydrolase / peptidyl-tRNA hydrolase activity / translation / 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 speciesStreptococcus pyogenes NZ131 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsSingh, A. / Gautam, L. / Sinha, M. / Bhushan, A. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: FEBS Open Bio / Year: 2014
Title: Crystal structure of peptidyl-tRNA hydrolase from a Gram-positive bacterium, Streptococcus pyogenes at 2.19 angstrom resolution shows the closed structure of the substrate-binding cleft.
Authors: Singh, A. / Gautam, L. / Sinha, M. / Bhushan, A. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionJul 7, 2014Deposition site: RCSB / Processing site: PDBJ
SupersessionAug 6, 2014ID: 4Q55
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2Nov 8, 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)42,4492
Polymers42,4492
Non-polymers00
Water5,062281
1
A: Peptidyl-tRNA hydrolase


Theoretical massNumber of molelcules
Total (without water)21,2251
Polymers21,2251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptidyl-tRNA hydrolase


Theoretical massNumber of molelcules
Total (without water)21,2251
Polymers21,2251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.024, 43.028, 65.100
Angle α, β, γ (deg.)90.33, 105.78, 112.51
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Peptidyl-tRNA hydrolase / PTH


Mass: 21224.510 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes NZ131 (bacteria)
Strain: NZ131 / Gene: pth, Spy49_0005 / Plasmid: pET28a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: B5XIP6, peptidyl-tRNA hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.1 Å3/Da / Density % sol: 41.35 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 26, 2013 / Details: Mirror
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.19→35.37 Å / Num. obs: 17325 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.062 / Net I/σ(I): 22.2
Reflection shellResolution: 2.19→2.23 Å / Mean I/σ(I) obs: 7.6 / Rsym value: 0.157 / % possible all: 97.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JC4

4jc4


Resolution: 2.19→35.37 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.919 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.371 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19847 884 5.1 %RANDOM
Rwork0.16844 ---
obs0.17002 16439 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.196 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å20.15 Å20.51 Å2
2---0.41 Å20.06 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 2.19→35.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2978 0 0 281 3259
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.014
X-RAY DIFFRACTIONr_bond_other_d0
X-RAY DIFFRACTIONr_angle_refined_deg1.589
X-RAY DIFFRACTIONr_angle_other_deg3.602
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.965
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.031
X-RAY DIFFRACTIONr_chiral_restr0.137
X-RAY DIFFRACTIONr_gen_planes_refined0.006
X-RAY DIFFRACTIONr_gen_planes_other0.009
X-RAY DIFFRACTIONr_mcbond_it1.066
X-RAY DIFFRACTIONr_mcbond_other1.064
X-RAY DIFFRACTIONr_mcangle_it1.687
X-RAY DIFFRACTIONr_mcangle_other1.687
X-RAY DIFFRACTIONr_scbond_it
LS refinement shellResolution: 2.193→2.25 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 64 -
Rwork0.197 1174 -
obs--92.46 %

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