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- PDB-7csn: Crystal structure of peptidyl-tRNA hydrolase from Acinetobacter b... -

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Basic information

Entry
Database: PDB / ID: 7csn
TitleCrystal structure of peptidyl-tRNA hydrolase from Acinetobacter baumannii at 1.00 A resolution
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 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 speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsViswanathan, V. / Sharma, P. / Singh, P.K. / Kaur, 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 peptidyl-tRNA hydrolase from Acinetobacter baumannii at 1.00 A resolution
Authors: Viswanathan, V. / Sharma, P. / Singh, P.K. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionAug 15, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2020Provider: 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

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Assembly

Deposited unit
A: Peptidyl-tRNA hydrolase


Theoretical massNumber of molelcules
Total (without water)21,2501
Polymers21,2501
Non-polymers00
Water4,306239
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.000, 66.250, 76.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptidyl-tRNA hydrolase / PTH


Mass: 21250.232 Da / Num. of mol.: 1
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, 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.: 239 / 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 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 12% PEG 1500, 0.1M HEPES, pH 7.5, 20% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1→33.15 Å / Num. obs: 90567 / % possible obs: 96.65 % / Redundancy: 9.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.04 / Net I/σ(I): 11.1
Reflection shellResolution: 1→1.02 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 6825 / CC1/2: 0.74 / Rpim(I) all: 0.42 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6j93

6j93


Resolution: 1→33.147 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.896 / SU ML: 0.02 / Cross valid method: FREE R-VALUE / ESU R: 0.024 / ESU R Free: 0.023
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1569 4520 5.054 %
Rwork0.1448 84906 -
all0.145 --
obs-89426 95.406 %
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: 15.225 Å2
Baniso -1Baniso -2Baniso -3
1--0.122 Å2-0 Å20 Å2
2--0.2 Å2-0 Å2
3----0.078 Å2
Refinement stepCycle: LAST / Resolution: 1→33.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1496 0 0 239 1735
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0131578
X-RAY DIFFRACTIONr_bond_other_d0.010.0171451
X-RAY DIFFRACTIONr_angle_refined_deg2.5141.6322144
X-RAY DIFFRACTIONr_angle_other_deg1.7941.5753391
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5645207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.86522.85784
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55215266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.941159
X-RAY DIFFRACTIONr_chiral_restr0.1580.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021813
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02314
X-RAY DIFFRACTIONr_nbd_refined0.2420.2322
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2080.21444
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2777
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0930.2706
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2460.2127
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2340.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3010.214
X-RAY DIFFRACTIONr_nbd_other0.2390.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1870.224
X-RAY DIFFRACTIONr_mcbond_it12.2421.212795
X-RAY DIFFRACTIONr_mcbond_other12.2491.21794
X-RAY DIFFRACTIONr_mcangle_it10.8961.789995
X-RAY DIFFRACTIONr_mcangle_other10.8921.79996
X-RAY DIFFRACTIONr_scbond_it14.9841.706783
X-RAY DIFFRACTIONr_scbond_other14.9841.704783
X-RAY DIFFRACTIONr_scangle_it13.7172.3081143
X-RAY DIFFRACTIONr_scangle_other13.7162.3061143
X-RAY DIFFRACTIONr_lrange_it14.60316.1761802
X-RAY DIFFRACTIONr_lrange_other14.69815.271748
X-RAY DIFFRACTIONr_rigid_bond_restr39.08333029
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.0260.372490.3554521X-RAY DIFFRACTION69.9927
1.026-1.0540.3152980.3095547X-RAY DIFFRACTION87.317
1.054-1.0850.2493330.2276033X-RAY DIFFRACTION98.3318
1.085-1.1180.1673400.1795897X-RAY DIFFRACTION98.7648
1.118-1.1550.1682880.1515709X-RAY DIFFRACTION97.9582
1.155-1.1950.1422940.145549X-RAY DIFFRACTION98.616
1.195-1.240.1512910.1355356X-RAY DIFFRACTION98.4141
1.24-1.2910.1462740.1355145X-RAY DIFFRACTION98.3842
1.291-1.3480.142580.1274958X-RAY DIFFRACTION97.8061
1.348-1.4140.1452600.1254777X-RAY DIFFRACTION99.0755
1.414-1.490.1492210.1254500X-RAY DIFFRACTION98.0681
1.49-1.580.1382180.1234279X-RAY DIFFRACTION97.9952
1.58-1.6890.1451970.1234028X-RAY DIFFRACTION97.5525
1.689-1.8240.1411840.1243803X-RAY DIFFRACTION98.933
1.824-1.9970.1481960.1263478X-RAY DIFFRACTION98.3668
1.997-2.2320.1361660.123084X-RAY DIFFRACTION96.2963
2.232-2.5750.1351460.1292839X-RAY DIFFRACTION99.0378
2.575-3.1490.1741400.1512434X-RAY DIFFRACTION99.7674
3.149-4.4340.135880.1311832X-RAY DIFFRACTION94.3489
4.434-33.140.16790.1951137X-RAY DIFFRACTION99.7539
Refinement TLS params.Method: refined / Origin x: 7.3331 Å / Origin y: 8.8338 Å / Origin z: 15.6639 Å
111213212223313233
T0.0142 Å2-0.0002 Å20.0001 Å2-0.0001 Å2-0.0002 Å2--0.0126 Å2
L0.0384 °2-0.0087 °20.0083 °2-0.0277 °2-0.0145 °2--0.0239 °2
S0.0001 Å °-0.002 Å °-0.0001 Å °0.0007 Å °0.0003 Å °0.0007 Å °-0.0003 Å °-0.001 Å °-0.0004 Å °
Refinement TLS groupSelection: ALL

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