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- PDB-7y52: Crystal structure of peptidyl-tRNA hydrolase from Enterococcus faecium -

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Basic information

Entry
Database: PDB / ID: 7y52
TitleCrystal structure of peptidyl-tRNA hydrolase from Enterococcus faecium
ComponentsPeptidyl-tRNA hydrolase
KeywordsHYDROLASE
Function / homology
Function and homology information


peptidyl-tRNA hydrolase / aminoacyl-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
DI(HYDROXYETHYL)ETHER / Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsPandey, R. / Zohib, M. / Mundra, S. / Pal, R.K. / Arora, A.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR)CSIR FBR MLP 2029 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. / Kaul, G. / Akhir, A. / Saxena, D. / Shukla, M. / Mundra, S. / Zohib, M. / Singh, S. / Pal, R.K. / Tripathi, S. / Jain, A. / Chopra, S. / Arora, A.
History
DepositionJun 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 2.0Aug 7, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Source and taxonomy
Category: atom_site / citation ...atom_site / citation / citation_author / entity_src_gen / pdbx_nonpoly_scheme / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _pdbx_nonpoly_scheme.auth_seq_num / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6837
Polymers42,3732
Non-polymers3105
Water5,170287
1
A: Peptidyl-tRNA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3394
Polymers21,1861
Non-polymers1523
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-11 kcal/mol
Surface area9190 Å2
MethodPISA
2
B: Peptidyl-tRNA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3453
Polymers21,1861
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area8760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.821, 74.835, 63.751
Angle α, β, γ (deg.)90.000, 104.851, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 32 or resid 36...
d_2ens_1(chain "B" and (resid 1 through 27 or (resid 28...

NCS oper: (Code: givenMatrix: (-0.542150362211, 0.831006460188, 0.124504007487), (0.819821603405, 0.490613355978, 0.295281346392), (0.184297377479, 0.262157963949, -0.94726325728)Vector: 3. ...NCS oper: (Code: given
Matrix: (-0.542150362211, 0.831006460188, 0.124504007487), (0.819821603405, 0.490613355978, 0.295281346392), (0.184297377479, 0.262157963949, -0.94726325728)
Vector: 3.63770874527, -7.80025788682, 31.6206241915)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Peptidyl-tRNA hydrolase / PTH


Mass: 21186.494 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium (bacteria) / Gene: pth, GKZ95_07520 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysS / References: UniProt: A0A6A8NIM3, peptidyl-tRNA hydrolase

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Non-polymers , 5 types, 292 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.11 Å3/Da / Density % sol: 41.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M Ammonium Sulfate, 0.1 M Tris-HCl pH 7.5, 15% PEG 4K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.92→35 Å / Num. obs: 26521 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 26.11 Å2 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.023 / Rrim(I) all: 0.061 / Χ2: 1.433 / Net I/σ(I): 15.4 / Num. measured all: 193162
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.92-1.997.10.29226170.9680.1180.3160.876100
1.99-2.077.20.21526380.9820.0860.2320.927100
2.07-2.167.20.16126430.990.0650.1741.038100
2.16-2.287.20.15426710.990.0620.1661.535100
2.28-2.427.30.10826320.9950.0430.1161.194100
2.42-2.617.30.0926380.9960.0360.0971.293100
2.61-2.877.40.07226520.9970.0280.0771.494100
2.87-3.287.40.05326580.9990.0210.0571.797100
3.28-4.137.40.04526620.9990.0180.0482.369100
4.13-357.40.03327100.9990.0130.0361.73299.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YLY

4yly


Resolution: 1.92→23.78 Å / SU ML: 0.2139 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.504
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2339 1332 5.03 %
Rwork0.184 25167 -
obs0.1865 26499 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.74 Å2
Refinement stepCycle: LAST / Resolution: 1.92→23.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2904 0 18 287 3209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133054
X-RAY DIFFRACTIONf_angle_d1.27764126
X-RAY DIFFRACTIONf_chiral_restr0.0762454
X-RAY DIFFRACTIONf_plane_restr0.0103537
X-RAY DIFFRACTIONf_dihedral_angle_d11.3271420
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.15671934982 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.990.32341050.25082216X-RAY DIFFRACTION86.86
1.99-2.070.31251540.24052515X-RAY DIFFRACTION100
2.07-2.170.31391350.23422545X-RAY DIFFRACTION100
2.17-2.280.31161400.22682542X-RAY DIFFRACTION99.93
2.28-2.420.27221400.21652524X-RAY DIFFRACTION99.96
2.42-2.610.28211400.20782533X-RAY DIFFRACTION100
2.61-2.870.22891060.20582571X-RAY DIFFRACTION100
2.87-3.290.2331240.19122575X-RAY DIFFRACTION100
3.29-4.140.2171430.15442548X-RAY DIFFRACTION100
4.14-23.780.15761450.13812598X-RAY DIFFRACTION100

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