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- PDB-5zk0: Crystal structure of Peptidyl-tRNA hydrolase mutant -M71A from Vi... -

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Basic information

Entry
Database: PDB / ID: 5zk0
TitleCrystal structure of Peptidyl-tRNA hydrolase mutant -M71A from Vibrio cholerae
ComponentsPeptidyl-tRNA hydrolase
KeywordsHYDROLASE / Peptidyl-tRNA hydrolase / Mutant M71A
Function / homology
Function and homology information


peptidyl-tRNA hydrolase / peptidyl-tRNA hydrolase activity / tRNA binding / 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
Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsShahid, S. / Kabra, A. / Pal, R.K. / Arora, A.
CitationJournal: Biochim. Biophys. Acta / Year: 2018
Title: Role of methionine 71 in substrate recognition and structural integrity of bacterial peptidyl-tRNA hydrolase.
Authors: Shahid, S. / Kabra, A. / Mundra, S. / Pal, R.K. / Tripathi, S. / Jain, A. / Arora, A.
History
DepositionMar 22, 2018Deposition site: PDBJ / Processing site: PDBJ
SupersessionJun 6, 2018ID: 5H6F
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)43,4784
Polymers43,4322
Non-polymers462
Water2,126118
1
A: Peptidyl-tRNA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7392
Polymers21,7161
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidyl-tRNA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7392
Polymers21,7161
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.709, 117.491, 201.618
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-355-

HOH

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Components

#1: Protein Peptidyl-tRNA hydrolase / PTH


Mass: 21716.047 Da / Num. of mol.: 2 / Mutation: M70A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 51.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.1M sodium citrate, 0.2M ammonium acetate, 20% polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.55→100.81 Å / Num. obs: 14447 / % possible obs: 97.3 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 26.96
Reflection shellResolution: 2.55→2.64 Å / Rmerge(I) obs: 0.206

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Processing

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

4zxp


Resolution: 2.55→100.81 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.888 / SU B: 11.121 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R: 0.715 / ESU R Free: 0.326 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26316 733 5.1 %RANDOM
Rwork0.18641 ---
obs0.19028 13681 97.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.039 Å2
Baniso -1Baniso -2Baniso -3
1-1.67 Å20 Å2-0 Å2
2---2.35 Å2-0 Å2
3---0.69 Å2
Refinement stepCycle: 1 / Resolution: 2.55→100.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2941 0 2 118 3061
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193002
X-RAY DIFFRACTIONr_bond_other_d0.0010.022928
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.9724062
X-RAY DIFFRACTIONr_angle_other_deg0.81336725
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5915387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.7924.64125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.88615500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3791514
X-RAY DIFFRACTIONr_chiral_restr0.0790.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213425
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02663
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_it2.2253.7351556
X-RAY DIFFRACTIONr_mcbond_other2.2253.7351555
X-RAY DIFFRACTIONr_mcangle_it3.5545.5911941
X-RAY DIFFRACTIONr_mcangle_other3.5535.5911942
X-RAY DIFFRACTIONr_scbond_it2.464.0021445
X-RAY DIFFRACTIONr_scbond_other2.4523.9991443
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0315.892121
X-RAY DIFFRACTIONr_long_range_B_refined5.75929.3423374
X-RAY DIFFRACTIONr_long_range_B_other5.75529.3383365
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.548→2.614 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 51 -
Rwork0.252 817 -
obs--79.71 %

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