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- PDB-6lsp: Crystal structure of a dimeric Piptidyl t-RNA hydrolase from Acin... -

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Basic information

Entry
Database: PDB / ID: 6lsp
TitleCrystal structure of a dimeric Piptidyl t-RNA hydrolase from Acinetobacter baumannii at 1.50 A resolution reveals an inhibited form.
ComponentsPeptidyl-tRNA hydrolase
KeywordsHYDROLASE
Function / homology
Function and homology information


peptidyl-tRNA hydrolase / peptidyl-tRNA hydrolase activity / protein quality control for misfolded or incompletely synthesized proteins / rescue of stalled ribosome / tRNA binding / 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 speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsViswanathan, V. / Ahmad, M.I. / Sharma, P. / Sharma, S. / Singh, T.P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)PDF/2018/000008 India
CitationJournal: To Be Published
Title: Crystal structure of a dimeric Piptidyl t-RNA hydrolase from Acinetobacter baumannii at 1.50 A resolution reveals on inhibited form.
Authors: Viswanathan, V. / Ahmad, M.I. / Sharma, P. / Sharma, S. / Singh, T.P.
History
DepositionJan 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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)41,9362
Polymers41,9362
Non-polymers00
Water11,205622
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint1 kcal/mol
Surface area16460 Å2
Unit cell
Length a, b, c (Å)34.580, 98.540, 123.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Peptidyl-tRNA hydrolase / PTH


Mass: 20967.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81) (bacteria)
Strain: ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81
Gene: pth, BIT33_16330, HMPREF0010_01329 / Production host: Escherichia coli (E. coli) / References: UniProt: D0C9L6, peptidyl-tRNA hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 622 / 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: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% PEG 1500, 0.1M HEPES, pH 7.5, 22% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.5→38.56 Å / Num. obs: 68761 / % possible obs: 99.97 % / Redundancy: 6.5 % / Biso Wilson estimate: 10.37 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.042 / Rrim(I) all: 0.108 / Net I/σ(I): 11.2
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 4972 / CC1/2: 0.86 / Rpim(I) all: 0.22 / Rrim(I) all: 0.58 / % possible all: 99.92

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YN4

5yn4


Resolution: 1.5→33.3 Å / SU ML: 0.1213 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.9696
RfactorNum. reflection% reflection
Rfree0.1968 1405 2.04 %
Rwork0.1696 --
obs0.1701 68759 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 15.2 Å2
Refinement stepCycle: LAST / Resolution: 1.5→33.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2952 0 0 622 3574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00573082
X-RAY DIFFRACTIONf_angle_d0.82134179
X-RAY DIFFRACTIONf_chiral_restr0.0562442
X-RAY DIFFRACTIONf_plane_restr0.0051561
X-RAY DIFFRACTIONf_dihedral_angle_d7.53392551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.550.22471330.2016614X-RAY DIFFRACTION99.96
1.55-1.620.20561490.18756624X-RAY DIFFRACTION99.99
1.62-1.690.23031430.18256629X-RAY DIFFRACTION100
1.69-1.780.21481300.17576677X-RAY DIFFRACTION99.99
1.78-1.890.20351250.17426702X-RAY DIFFRACTION100
1.89-2.040.1981400.17366726X-RAY DIFFRACTION99.97
2.04-2.240.17971410.16586691X-RAY DIFFRACTION100
2.24-2.560.19741440.17016757X-RAY DIFFRACTION99.96
2.56-3.230.20441530.16786820X-RAY DIFFRACTION100
3.23-33.30.17951470.15667114X-RAY DIFFRACTION99.96

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