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- PDB-4lwq: Crystal structure of native peptidyl t-RNA hydrolase from Acineto... -

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Basic information

Entry
Database: PDB / ID: 4lwq
TitleCrystal structure of native peptidyl t-RNA hydrolase from Acinetobacter baumannii at 1.38A resolution
ComponentsPeptidyl-tRNA hydrolase
KeywordsHYDROLASE / Protein synthesis
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: 1.38 Å
AuthorsKaushik, S. / Singh, N. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To be Published
Title: Crystal structure of native peptidyl t-RNA hydrolase from Acinetobacter baumannii at 1.38A resolution
Authors: Kaushik, S. / Singh, N. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionJul 28, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-tRNA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4343
Polymers21,2501
Non-polymers1842
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.980, 65.980, 75.890
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 (bacteria) / Strain: ATCC 19606 / Gene: pth / Production host: Escherichia coli (E. coli) / References: UniProt: D0C9L6, peptidyl-tRNA hydrolase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 38.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50mM HEPES, PEG 400, PEG 1500, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 23, 2013 / Details: Mirror
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.38→25.31 Å / Num. all: 34019 / Num. obs: 34019 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.38→1.4 Å / % possible all: 97.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JWK

4jwk


Resolution: 1.38→25.31 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.304 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.055 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15242 1793 5 %RANDOM
Rwork0.12978 ---
obs0.13091 34019 99.98 %-
all-34019 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.079 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0 Å20 Å2
2--0.09 Å2-0 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.38→25.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1496 0 12 200 1708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191542
X-RAY DIFFRACTIONr_bond_other_d0.0010.021491
X-RAY DIFFRACTIONr_angle_refined_deg1.1171.9552080
X-RAY DIFFRACTIONr_angle_other_deg0.74633427
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4685195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.41323.91369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.12515254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.933159
X-RAY DIFFRACTIONr_chiral_restr0.0720.2220
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211776
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02365
X-RAY DIFFRACTIONr_mcbond_it0.820.975783
X-RAY DIFFRACTIONr_mcbond_other0.8190.973782
X-RAY DIFFRACTIONr_mcangle_it1.1391.468977
X-RAY DIFFRACTIONr_mcangle_other1.1391.469978
X-RAY DIFFRACTIONr_scbond_it1.0371.212759
X-RAY DIFFRACTIONr_scbond_other1.0371.212759
X-RAY DIFFRACTIONr_scangle_other1.2121.7221104
X-RAY DIFFRACTIONr_long_range_B_refined2.4679.5661855
X-RAY DIFFRACTIONr_long_range_B_other2.4679.561855
X-RAY DIFFRACTIONr_rigid_bond_restr1.07433033
X-RAY DIFFRACTIONr_sphericity_free24.045540
X-RAY DIFFRACTIONr_sphericity_bonded5.44153159
LS refinement shellResolution: 1.381→1.417 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.203 106 -
Rwork0.155 2514 -
obs--100 %

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