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- PDB-6jqt: Crystal structure of ordered Asn70 and Asn116 in native peptidyl ... -

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Basic information

Entry
Database: PDB / ID: 6jqt
TitleCrystal structure of ordered Asn70 and Asn116 in native peptidyl t-RNA hydrolase from Acinetobacter baumannii at 1.80 Angstrom 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 / 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: 1.8 Å
AuthorsViswanathan, V. / Sharma, P. / Sharma, S. / Singh, T.P.
CitationJournal: To Be Published
Title: Crystal structure of ordered Asn70 and Asn116 in native peptidyl t-RNA hydrolase from Acinetobacter baumannii at 1.80 Angstrom resolution.
Authors: Viswanathan, V. / Sharma, P. / Sharma, S. / Singh, T.P.
History
DepositionApr 1, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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


Theoretical massNumber of molelcules
Total (without water)21,2501
Polymers21,2501
Non-polymers00
Water4,270237
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.918, 66.290, 75.968
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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.: 237 / 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: 2.01 Å3/Da / Density % sol: 38.79 %
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: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.8→49.95 Å / Num. obs: 16506 / % possible obs: 87.16 % / Redundancy: 2.3 % / CC1/2: 0.9 / Rrim(I) all: 0.143 / Net I/σ(I): 12.57
Reflection shellResolution: 1.8→1.88 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 3.23 / Num. unique obs: 3101 / CC1/2: 0.88 / Rrim(I) all: 0.383 / % possible all: 81.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Coot0.8.9model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J93

6j93


Resolution: 1.8→49.95 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.897 / SU B: 2.635 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.17 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2483 692 4.8 %RANDOM
Rwork0.20536 ---
obs0.20747 13694 87.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.12 Å2-0 Å2
3----0.1 Å2
Refinement stepCycle: 1 / Resolution: 1.8→49.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1496 0 0 237 1733
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131542
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171422
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.6322085
X-RAY DIFFRACTIONr_angle_other_deg1.4191.5753312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3135195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.34822.580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54715257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.983159
X-RAY DIFFRACTIONr_chiral_restr0.0790.2192
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021755
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02308
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2061.176783
X-RAY DIFFRACTIONr_mcbond_other1.1741.174782
X-RAY DIFFRACTIONr_mcangle_it1.9291.76977
X-RAY DIFFRACTIONr_mcangle_other1.931.761978
X-RAY DIFFRACTIONr_scbond_it1.5291.349759
X-RAY DIFFRACTIONr_scbond_other1.5281.349759
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4131.9421108
X-RAY DIFFRACTIONr_long_range_B_refined5.47515.7311819
X-RAY DIFFRACTIONr_long_range_B_other5.09815.031763
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 48 -
Rwork0.12 805 -
obs--72.6 %

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