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- PDB-8iu6: Crystal structure of peptidyl-tRNA hydrolase mutant from Enteroco... -

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Basic information

Entry
Database: PDB / ID: 8iu6
TitleCrystal structure of peptidyl-tRNA hydrolase mutant from Enterococcus faecium
ComponentsPeptidyl-tRNA hydrolase
KeywordsHYDROLASE / Peptidyl tRNA Hydrolase
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
Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPandey, R. / Tripathi, S. / Lanka, A.K. / Zohib, M. / Pal, R.K. / Arora, A.
Funding support India, 2items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR)CSIR FBR MLP 2029 India
Department of Biotechnology (DBT, India)BT/PR31893/MED/29/1390/2019 India
CitationJournal: To Be Published
Title: Crystal structure of peptidyl-tRNA hydrolase mutant from Enterococcus faecium
Authors: Pandey, R. / Tripathi, S. / Lanka, A.K. / Zohib, M. / Pal, R.K. / Arora, A.
History
DepositionMar 23, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2024Provider: 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
B: Peptidyl-tRNA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9904
Polymers41,8062
Non-polymers1842
Water1,33374
1
A: Peptidyl-tRNA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9952
Polymers20,9031
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidyl-tRNA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9952
Polymers20,9031
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.739, 49.435, 65.500
Angle α, β, γ (deg.)90.000, 107.868, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-338-

HOH

21A-340-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 1 / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 186 / Label seq-ID: 1 - 186

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Peptidyl-tRNA hydrolase


Mass: 20903.125 Da / Num. of mol.: 2 / Mutation: H19N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium (bacteria) / Gene: pth / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A133CPV0
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
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: 2.41 Å3/Da / Density % sol: 48.95 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Tris-HCl pH 7.5 0.2M Ammonium Sulfate 25% 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 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.9→62.34 Å / Num. obs: 9021 / % possible obs: 93 % / Redundancy: 2.1 % / CC1/2: 0.98 / Net I/σ(I): 21.7
Reflection shellResolution: 2.9→3.01 Å / Num. unique obs: 861 / CC1/2: 0.95

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7Y52

7y52


Resolution: 2.9→32.11 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.851 / SU ML: 0.472 / Cross valid method: THROUGHOUT / ESU R Free: 0.502
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.286 445 5.073 %RANDOM
Rwork0.235 8327 --
all0.238 ---
obs-8772 97.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 41.49 Å2
Baniso -1Baniso -2Baniso -3
1-4.753 Å2-0 Å20.189 Å2
2---0.236 Å20 Å2
3----3.84 Å2
Refinement stepCycle: LAST / Resolution: 2.9→32.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2794 0 12 74 2880
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0122870
X-RAY DIFFRACTIONr_bond_other_d0.0040.0162590
X-RAY DIFFRACTIONr_angle_refined_deg0.8811.6343877
X-RAY DIFFRACTIONr_angle_other_deg0.3281.5456005
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8235372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.5911012
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.091930.0501
12AX-RAY DIFFRACTIONLocal ncs0.091930.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.9750.28225577X-RAY DIFFRACTION93.1889
2.975-3.0560.456330.276570X-RAY DIFFRACTION95.7143
3.056-3.1430.363300.259567X-RAY DIFFRACTION96.1353
3.143-3.2390.331250.242564X-RAY DIFFRACTION96.875
3.239-3.3440.356320.26541X-RAY DIFFRACTION97.2835
3.344-3.460.333250.261516X-RAY DIFFRACTION97.4775
3.46-3.5890.273190.264528X-RAY DIFFRACTION97.6786
3.589-3.7340.235300.216481X-RAY DIFFRACTION97.5191
3.734-3.8970.279250.211473X-RAY DIFFRACTION97.6471
3.897-4.0850.21230.19468X-RAY DIFFRACTION98.5944
4.085-4.3020.265280.198422X-RAY DIFFRACTION98.0392
4.302-4.5580.25300.189402X-RAY DIFFRACTION98.4055
4.558-4.8650.365130.194388X-RAY DIFFRACTION98.2843
4.865-5.2450.281180.224361X-RAY DIFFRACTION98.1865
5.245-5.730.288190.253338X-RAY DIFFRACTION98.892
5.73-6.3810.341200.251310X-RAY DIFFRACTION98.5075
6.381-7.3210.277100.254284X-RAY DIFFRACTION99.3243
7.321-8.8520.234170.229228X-RAY DIFFRACTION98.3936
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.5659-0.5735-0.91554.08890.21374.8718-0.0694-0.0023-0.0114-0.0708-0.01540.13810.1175-0.08990.08480.0231-0.02790.03210.1354-0.02150.07949.43110.307428.3046
22.2261-0.0799-0.62233.52920.68285.32290.1071-0.0268-0.09020.0128-0.05670.0957-0.1583-0.1016-0.05030.02020.01770.02980.14910.00590.10630.0754-9.019656.9811
Refinement TLS groupSelection: ALL

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