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- PDB-6jj1: Crystal structure of peptidyl-tRNA hydrolase from Acinetobacter b... -

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Basic information

Entry
Database: PDB / ID: 6jj1
TitleCrystal structure of peptidyl-tRNA hydrolase from Acinetobacter baumannii at 0.97 A resolution with disordered five N-terminal residues
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: 0.97 Å
AuthorsIqbal, N. / Sharma, P. / Chaudhary, A. / Sharma, S. / Singh, T.P.
CitationJournal: To Be Published
Title: Crystal structure of peptidyl-tRNA hydrolase from Acinetobacter baumannii at 0.97 A resolution with disordered five N-terminal residues
Authors: Iqbal, N. / Sharma, P. / Chaudhary, A. / Sharma, S. / Singh, T.P.
History
DepositionFeb 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 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

Downloads & links

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Assembly

Deposited unit
A: Peptidyl-tRNA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4195
Polymers21,2501
Non-polymers1684
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-11 kcal/mol
Surface area8900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.986, 66.131, 76.103
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 BL21 (bacteria) / References: UniProt: D0C9L6, peptidyl-tRNA hydrolase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 38.87 %
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: 0.97199 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97199 Å / Relative weight: 1
ReflectionResolution: 0.97→38.08 Å / Num. obs: 94081 / % possible obs: 92 % / Redundancy: 8.3 % / Rpim(I) all: 0.028 / Net I/σ(I): 14.9
Reflection shellResolution: 0.97→1 Å / Num. unique obs: 3426 / Rpim(I) all: 0.629

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y9A

5y9a


Resolution: 0.97→38.08 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.578 / SU ML: 0.014 / Cross valid method: THROUGHOUT / ESU R: 0.02 / ESU R Free: 0.023 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.16705 1170 1.2 %RANDOM
Rwork0.13378 ---
obs0.13418 92828 92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.612 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0 Å20 Å2
2--0.1 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 0.97→38.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1496 0 7 252 1755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0121562
X-RAY DIFFRACTIONr_bond_other_d0.0030.0171516
X-RAY DIFFRACTIONr_angle_refined_deg2.0061.6262114
X-RAY DIFFRACTIONr_angle_other_deg0.7231.5743455
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4855201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.41522.580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.52815258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.085159
X-RAY DIFFRACTIONr_chiral_restr0.130.2193
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021843
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02380
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_it6.281.18798
X-RAY DIFFRACTIONr_mcbond_other6.284797
X-RAY DIFFRACTIONr_mcangle_it8.4041.7571001
X-RAY DIFFRACTIONr_mcangle_other8.414.141002
X-RAY DIFFRACTIONr_scbond_it8.0521.48764
X-RAY DIFFRACTIONr_scbond_other8.061761
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.512.0471111
X-RAY DIFFRACTIONr_long_range_B_refined8.76615.4791777
X-RAY DIFFRACTIONr_long_range_B_other8.76414.4371711
X-RAY DIFFRACTIONr_rigid_bond_restr35.01931562
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 0.97→0.995 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 42 -
Rwork0.273 3380 -
obs--46.01 %
Refinement TLS params.Method: refined / Origin x: 7.2995 Å / Origin y: 8.8951 Å / Origin z: 15.461 Å
111213212223313233
T0.0002 Å2-0 Å20.0001 Å2-0.0001 Å20.0001 Å2--0.004 Å2
L0.0142 °2-0.0037 °20.0086 °2-0.03 °2-0.0109 °2--0.0146 °2
S0.0008 Å °-0.0011 Å °-0.0003 Å °0.0019 Å °0.0011 Å °0.0018 Å °-0.0005 Å °-0.0005 Å °-0.0019 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 193
2X-RAY DIFFRACTION1A301 - 552

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