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- PDB-7brd: Crystal structure of Peptidyl-tRNA hydrolase from Klebsiella pneu... -

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Basic information

Entry
Database: PDB / ID: 7brd
TitleCrystal structure of Peptidyl-tRNA hydrolase from Klebsiella pneumoniae
ComponentsPeptidyl-tRNA hydrolase
KeywordsHYDROLASE / tRNA-binding / Antibiotic target
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
ACETATE ION / BETA-MERCAPTOETHANOL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.892 Å
AuthorsMundra, S. / Zohib, M. / Pal, R.K. / Biswal, B.K. / Arora, A.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)GAP328 India
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2021
Title: Structural and functional characterization of peptidyl-tRNA hydrolase from Klebsiella pneumoniae.
Authors: Mundra, S. / Pal, R.K. / Tripathi, S. / Jain, A. / Arora, A.
History
DepositionMar 27, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)44,11531
Polymers42,1202
Non-polymers1,99529
Water5,368298
1
A: Peptidyl-tRNA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,31220
Polymers21,0601
Non-polymers1,25219
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidyl-tRNA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,80311
Polymers21,0601
Non-polymers74310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.203, 72.372, 77.415
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Peptidyl-tRNA hydrolase / PTH


Mass: 21060.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: pth, BL124_00016980, EAO17_03025, F3P37_02700, SAMEA3538476_04832, SK89_03098
Production host: Escherichia coli (E. coli) / References: UniProt: A0A2V3K250, peptidyl-tRNA hydrolase

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Non-polymers , 8 types, 327 molecules

#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


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


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.34 Å3/Da / Density % sol: 47.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Ammonium Sulfate 0.1M Sodium cacodylate 30% PEG 8000

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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: Dec 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.89→31.97 Å / Num. obs: 31852 / % possible obs: 100 % / Redundancy: 10.6 % / Biso Wilson estimate: 22.06 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.049 / Rrim(I) all: 0.163 / Net I/σ(I): 10.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.127 / Num. unique obs: 31899 / CC1/2: 0.827 / Rpim(I) all: 0.271 / Rrim(I) all: 0.89 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PTH

2pth


Resolution: 1.892→25.208 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.924 / SU B: 6.264 / SU ML: 0.095 / Cross valid method: FREE R-VALUE / ESU R: 0.147 / ESU R Free: 0.141
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2218 1537 4.825 %
Rwork0.1738 --
all0.176 --
obs-31852 99.116 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.807 Å2
Baniso -1Baniso -2Baniso -3
1--0.348 Å2-0 Å2-0 Å2
2--0.071 Å2-0 Å2
3---0.277 Å2
Refinement stepCycle: LAST / Resolution: 1.892→25.208 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2877 0 120 298 3295
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0133045
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172853
X-RAY DIFFRACTIONr_angle_refined_deg1.7921.6444093
X-RAY DIFFRACTIONr_angle_other_deg1.4831.5726578
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7215389
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.92322.015134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59415456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7041518
X-RAY DIFFRACTIONr_chiral_restr0.0940.2384
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023413
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02607
X-RAY DIFFRACTIONr_nbd_refined0.2170.2624
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.22634
X-RAY DIFFRACTIONr_nbtor_refined0.1650.21493
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21431
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2198
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3130.214
X-RAY DIFFRACTIONr_nbd_other0.2290.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1670.223
X-RAY DIFFRACTIONr_mcbond_it1.4621.7241561
X-RAY DIFFRACTIONr_mcbond_other1.4411.7171557
X-RAY DIFFRACTIONr_mcangle_it2.2592.5531937
X-RAY DIFFRACTIONr_mcangle_other2.2592.5551938
X-RAY DIFFRACTIONr_scbond_it1.9721.9651484
X-RAY DIFFRACTIONr_scbond_other1.9711.9671485
X-RAY DIFFRACTIONr_scangle_it2.9282.8162154
X-RAY DIFFRACTIONr_scangle_other2.9272.8182155
X-RAY DIFFRACTIONr_lrange_it5.8433.39913238
X-RAY DIFFRACTIONr_lrange_other5.83933.40213239
X-RAY DIFFRACTIONr_ncsr_local_group_10.1240.055728
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.892-1.9410.3891130.3232055X-RAY DIFFRACTION92.9276
1.941-1.9940.2461070.2232145X-RAY DIFFRACTION99.6901
1.994-2.0520.26900.1972156X-RAY DIFFRACTION99.9555
2.052-2.1150.191980.1682035X-RAY DIFFRACTION99.9531
2.115-2.1840.232670.1562028X-RAY DIFFRACTION100
2.184-2.2610.243800.1551963X-RAY DIFFRACTION100
2.261-2.3460.231140.1481850X-RAY DIFFRACTION100
2.346-2.4420.191950.1411782X-RAY DIFFRACTION100
2.442-2.550.171030.1441700X-RAY DIFFRACTION100
2.55-2.6740.2281070.1541648X-RAY DIFFRACTION100
2.674-2.8180.213980.1641542X-RAY DIFFRACTION100
2.818-2.9890.2670.1611510X-RAY DIFFRACTION100
2.989-3.1940.218630.1531423X-RAY DIFFRACTION100
3.194-3.4490.197800.1591305X-RAY DIFFRACTION100
3.449-3.7770.231750.2021164X-RAY DIFFRACTION96.6459
3.777-4.220.227470.1781093X-RAY DIFFRACTION96.7742
4.22-4.8670.219580.175972X-RAY DIFFRACTION99.2293
4.867-5.9490.219270.184869X-RAY DIFFRACTION100
5.949-8.360.268300.198677X-RAY DIFFRACTION100
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)
10.44-0.0284-0.03060.2528-0.16150.48020.01390.00030.003-0.00560.00280.0006-0.00440.0168-0.01670.0007-0.0006-0.00140.06330.01110.0467-6.419-6.358826.5727
21.1299-0.30540.03910.17080.09890.2325-0.0455-0.08860.03520.00530.0132-0.0304-0.0092-0.0420.03240.00620.0081-0.00130.07580.00330.0489-28.859815.65522.0288
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 712
2X-RAY DIFFRACTION2ALLB1 - 308

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