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- PDB-9ls8: Crystal structure of peptidyl-tRNA hydrolase from Enterococcus fa... -

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Basic information

Entry
Database: PDB / ID: 9ls8
TitleCrystal structure of peptidyl-tRNA hydrolase from Enterococcus faecium at 1.22 A
ComponentsPeptidyl-tRNA hydrolase
KeywordsHYDROLASE / peptidyl-tRNA hydrolase / Enterococcus faecium
Function / homology
Function and homology information


peptidyl-tRNA hydrolase / peptidyl-tRNA hydrolase activity / translation / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsPandey, R. / Zohib, M. / Arora, A.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)GAP0438 India
CitationJournal: Int J Biol Macromol / Year: 2024
Title: Characterization of structure of peptidyl-tRNA hydrolase from Enterococcus faecium and its inhibition by a pyrrolinone compound.
Authors: Pandey, R. / Zohib, M. / Arora, A.
History
DepositionFeb 4, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release

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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)21,5657
Polymers21,1861
Non-polymers3786
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-13 kcal/mol
Surface area8980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.765, 47.584, 69.168
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: 21186.494 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium (bacteria)
Gene: pth, AWT83_04625, B1P95_10305, CQR37_02495, CUN04_03690, CUS10_01235, CYQ77_06165, EB12_02316, GBM44_12820, GBM73_11110, KYX88_05820, M3X98_03560, P6Z85_03115
Production host: Escherichia coli (E. coli) / References: UniProt: A0A133CPV0, peptidyl-tRNA hydrolase

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Non-polymers , 5 types, 147 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 1.82 Å3/Da / Density % sol: 32.28 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M Ammonium Sulphate, 0.1M Tris-HCl pH 7.5, 15% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.885 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Sep 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.885 Å / Relative weight: 1
ReflectionResolution: 1.22→47.58 Å / Num. obs: 40928 / % possible obs: 88.7 % / Redundancy: 4.3 % / CC1/2: 0.997 / Net I/σ(I): 13.4
Reflection shellResolution: 1.22→1.24 Å / Num. unique obs: 2262 / CC1/2: 0.71

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.22→30.06 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.948 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19805 1981 4.8 %RANDOM
Rwork0.15838 ---
obs0.16019 38903 88.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.027 Å2
Baniso -1Baniso -2Baniso -3
1-1.51 Å2-0 Å20 Å2
2---1 Å2-0 Å2
3----0.51 Å2
Refinement stepCycle: 1 / Resolution: 1.22→30.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1464 0 12 141 1617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0121513
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161432
X-RAY DIFFRACTIONr_angle_refined_deg1.6571.6572040
X-RAY DIFFRACTIONr_angle_other_deg0.581.5683296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0825192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.42256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81410244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0860.2225
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021746
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02338
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.621.768762
X-RAY DIFFRACTIONr_mcbond_other4.6151.767762
X-RAY DIFFRACTIONr_mcangle_it6.3933.188953
X-RAY DIFFRACTIONr_mcangle_other6.3963.188954
X-RAY DIFFRACTIONr_scbond_it7.2252.132751
X-RAY DIFFRACTIONr_scbond_other7.0142.119744
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.5763.7261075
X-RAY DIFFRACTIONr_long_range_B_refined12.34623.111712
X-RAY DIFFRACTIONr_long_range_B_other12.01522.051690
X-RAY DIFFRACTIONr_rigid_bond_restr3.73332945
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.223→1.255 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 169 -
Rwork0.243 3099 -
obs--96.57 %

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