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- PDB-4zxp: Crystal structure of Peptidyl- tRNA Hydrolase from Vibrio cholerae -

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Basic information

Entry
Database: PDB / ID: 4zxp
TitleCrystal structure of Peptidyl- tRNA Hydrolase from Vibrio cholerae
ComponentsPeptidyl-tRNA hydrolaseAlternative ribosome-rescue factor B
KeywordsHYDROLASE / PEPTIDYL-TRNA
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
CITRATE ANION / Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsShahid, S. / Pal, R.K. / Kabra, A. / Yadav, R. / Kumar, A. / Arora, A.
CitationJournal: RNA / Year: 2017
Title: Unraveling the stereochemical and dynamic aspects of the catalytic site of bacterial peptidyl-tRNA hydrolase.
Authors: Kabra, A. / Shahid, S. / Pal, R.K. / Yadav, R. / Pulavarti, S.V. / Jain, A. / Tripathi, S. / Arora, A.
History
DepositionMay 20, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Nov 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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-tRNA hydrolase
B: Peptidyl-tRNA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7093
Polymers43,5202
Non-polymers1891
Water5,963331
1
A: Peptidyl-tRNA hydrolase


Theoretical massNumber of molelcules
Total (without water)21,7601
Polymers21,7601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidyl-tRNA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9492
Polymers21,7601
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-11 kcal/mol
Surface area16230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.718, 73.628, 124.201
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 / Alternative ribosome-rescue factor B / PTH


Mass: 21760.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: pth, VC_2184 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KQ21, peptidyl-tRNA hydrolase
#2: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHESE RESIDUES ARE THE OVERHANGS LEFT AFTER RTEV DIGESTION.

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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: 2.38 Å3/Da / Density % sol: 48.43 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M SODIUM CITRATE BUFFER PH 8.0, 0.2M AMMONIUM ACETATE, 25% POLYETHYLENE GLYCOL 4000

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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: Jan 23, 2014
RadiationMonochromator: MULTI-MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.627→63.34 Å / Num. obs: 49768 / % possible obs: 95 % / Redundancy: 11 % / Net I/σ(I): 32.3
Reflection shellResolution: 1.63→1.69 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P7B

4p7b


Resolution: 1.63→32.55 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.211 1917 4.03 %
Rwork0.171 --
obs0.173 45683 91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.74 Å2
Refinement stepCycle: LAST / Resolution: 1.63→32.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2957 0 13 331 3301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113037
X-RAY DIFFRACTIONf_angle_d1.2664111
X-RAY DIFFRACTIONf_dihedral_angle_d16.741122
X-RAY DIFFRACTIONf_chiral_restr0.051459
X-RAY DIFFRACTIONf_plane_restr0.007542
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6273-1.6680.34741170.2993284080
1.668-1.71310.31911300.256306386
1.7131-1.76350.28111270.2325304487
1.7635-1.82040.27181330.223307187
1.8204-1.88550.27261270.2228299184
1.8855-1.9610.28041310.2231313788
1.961-2.05020.22241330.1997325792
2.0502-2.15830.23381390.1915334794
2.1583-2.29350.22761400.1895326492
2.2935-2.47050.20621410.186338694
2.4705-2.7190.21761410.1902338395
2.719-3.11220.22421480.1823349196
3.1122-3.920.1941520.149361999
3.920.17471580.1362379099

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