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- PDB-5gvz: Crystal structure of Peptidyl-tRNA hydrolase from Vibrio cholerae... -

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Basic information

Entry
Database: PDB / ID: 5gvz
TitleCrystal structure of Peptidyl-tRNA hydrolase from Vibrio cholerae in space group C2221 at resolution 1.75A.
ComponentsPeptidyl-tRNA hydrolaseAlternative ribosome-rescue factor B
KeywordsHYDROLASE / Peptidyl-tRNA hydrolase / Vibrio cholerae
Function / homology
Function and homology information


peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / translation / 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
ACETATE ION / Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsShahid, S. / Kabra, A. / Pal, R.K. / Arora, A.
CitationJournal: To Be Published
Title: Crystal structure of Peptidyl-tRNA hydrolase from Vibrio cholerae in space group C2221 at resolution 1.75A.
Authors: Shahid, S. / Kabra, A. / Pal, R.K. / Arora, A.
History
DepositionSep 7, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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)21,8624
Polymers21,6481
Non-polymers2143
Water2,504139
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.136, 73.462, 120.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Peptidyl-tRNA hydrolase / Alternative ribosome-rescue factor B / PTH


Mass: 21648.037 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: ATCC 39541 / Classical Ogawa 395 / O395 / Gene: pth, VC0395_A1761, VC395_2298
Production host: Escherichia coli BL21-Gold(DE3)pLysS AG (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: A5F686, peptidyl-tRNA hydrolase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.36 Å3/Da / Density % sol: 47.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 100 mM sodium acetate (pH 5.6), 200 mM potassium sodium tartrate, 2M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 20981 / % possible obs: 99.3 % / Redundancy: 12.9 % / Net I/σ(I): 50.1
Reflection shellResolution: 1.75→1.81 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZXP

4zxp


Resolution: 1.75→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.916 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.121 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23499 1072 5.1 %RANDOM
Rwork0.191 ---
obs0.1932 19759 98.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.978 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å2-0 Å2-0 Å2
2---0.35 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1482 0 13 139 1634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191522
X-RAY DIFFRACTIONr_bond_other_d0.0010.021492
X-RAY DIFFRACTIONr_angle_refined_deg1.8971.9792055
X-RAY DIFFRACTIONr_angle_other_deg0.91933426
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5375193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.84424.46265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.95815259
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.901158
X-RAY DIFFRACTIONr_chiral_restr0.110.2228
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211730
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02338
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_it1.6491.75777
X-RAY DIFFRACTIONr_mcbond_other1.6061.738774
X-RAY DIFFRACTIONr_mcangle_it2.3022.601967
X-RAY DIFFRACTIONr_mcangle_other2.3012.604968
X-RAY DIFFRACTIONr_scbond_it2.6352.088743
X-RAY DIFFRACTIONr_scbond_other2.6342.091744
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9813.0191087
X-RAY DIFFRACTIONr_long_range_B_refined6.01615.3071774
X-RAY DIFFRACTIONr_long_range_B_other6.01515.3241775
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.749→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 71 -
Rwork0.227 1319 -
obs--90.03 %
Refinement TLS params.Method: refined / Origin x: 15.0154 Å / Origin y: 11.7226 Å / Origin z: -11.8142 Å
111213212223313233
T0.0195 Å20.0052 Å20.0011 Å2-0.0136 Å2-0.0021 Å2--0.0396 Å2
L0.9297 °2-0.5114 °2-0.0534 °2-2.4698 °2-0.3505 °2--0.8287 °2
S0.0127 Å °0.0564 Å °0.1205 Å °-0.082 Å °-0.0351 Å °-0.1418 Å °-0.025 Å °-0.0761 Å °0.0224 Å °

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