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- PDB-5zzv: Crystal structure of PEG-1500 crystallized Peptidyl-tRNA Hydrolas... -

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Basic information

Entry
Database: PDB / ID: 5zzv
TitleCrystal structure of PEG-1500 crystallized Peptidyl-tRNA Hydrolase from Acinetobacter baumannii at 1.5 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 / 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: 1.57 Å
AuthorsBairagya, H.R. / Sharma, P. / Iqbal, N. / Sharma, S. / Singh, T.P.
CitationJournal: To Be Published
Title: Crystal structure of PEG-1500 crystallized Peptidyl-tRNA Hydrolase from Acinetobacter baumannii at 1.5 A resolution
Authors: Bairagya, H.R. / Sharma, P. / Iqbal, N. / Sharma, S. / Singh, T.P.
History
DepositionJun 4, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2018Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0302
Polymers20,9681
Non-polymers621
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint3 kcal/mol
Surface area8680 Å2
Unit cell
Length a, b, c (Å)109.025, 34.383, 58.659
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Peptidyl-tRNA hydrolase / PTH


Mass: 20967.957 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, BIT33_16330, HMPREF0010_01329 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: D0C9L6, peptidyl-tRNA hydrolase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.62 Å3/Da / Density % sol: 53.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100mM HEPES, 15% PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9095 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9095 Å / Relative weight: 1
ReflectionResolution: 1.57→39.93 Å / Num. obs: 24836 / % possible obs: 99.5 % / Redundancy: 12 % / Biso Wilson estimate: 26.8 Å2 / Rrim(I) all: 0.145 / Rsym value: 0.151 / Net I/σ(I): 8.7
Reflection shellResolution: 1.57→1.63 Å / Redundancy: 12 % / Mean I/σ(I) obs: 8.7 / Num. unique obs: 24836 / Rrim(I) all: 0.145 / Rsym value: 0.151 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FOP

4fop


Resolution: 1.57→39.93 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.536 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.094 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20544 1242 5 %RANDOM
Rwork0.17001 ---
obs0.17177 23593 78.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.875 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0 Å2-0 Å2
2---1.16 Å20 Å2
3---1.36 Å2
Refinement stepCycle: 1 / Resolution: 1.57→39.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1475 0 4 137 1616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191513
X-RAY DIFFRACTIONr_bond_other_d0.0050.021405
X-RAY DIFFRACTIONr_angle_refined_deg1.8881.9532042
X-RAY DIFFRACTIONr_angle_other_deg1.07233268
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8095192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7323.97168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66115252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.073159
X-RAY DIFFRACTIONr_chiral_restr0.1250.2216
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211703
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02294
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_it2.6082.814771
X-RAY DIFFRACTIONr_mcbond_other2.5712.808770
X-RAY DIFFRACTIONr_mcangle_it3.5074.201962
X-RAY DIFFRACTIONr_mcangle_other3.5054.208963
X-RAY DIFFRACTIONr_scbond_it3.9063.247742
X-RAY DIFFRACTIONr_scbond_other3.9063.247742
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8334.6741081
X-RAY DIFFRACTIONr_long_range_B_refined7.45335.5051719
X-RAY DIFFRACTIONr_long_range_B_other7.45335.5161720
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.57→1.609 Å
RfactorNum. reflection% reflection
Rfree0.365 28 -
Rwork0.35 529 -
obs--24.26 %

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