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- PDB-5b6j: Crystal structure of Peptidyl-tRNA hydrolase mutant -H24N from Vi... -

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Basic information

Entry
Database: PDB / ID: 5b6j
TitleCrystal structure of Peptidyl-tRNA hydrolase mutant -H24N from Vibrio cholerae
ComponentsPeptidyl-tRNA hydrolase
KeywordsHYDROLASE / Peptidyl-tRNA hydrolase / Mutant H24N
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 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsShahid, S. / Kabra, A. / Pal, R.K. / 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 30, 2016Deposition site: PDBJ / Processing site: PDBJ
SupersessionApr 12, 2017ID: 4Y2Z
Revision 1.0Apr 12, 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
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 30, 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


Theoretical massNumber of molelcules
Total (without water)43,4722
Polymers43,4722
Non-polymers00
Water1,928107
1
A: Peptidyl-tRNA hydrolase


Theoretical massNumber of molelcules
Total (without water)21,7361
Polymers21,7361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidyl-tRNA hydrolase


Theoretical massNumber of molelcules
Total (without water)21,7361
Polymers21,7361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.569, 72.628, 124.183
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: 21736.123 Da / Num. of mol.: 2 / Mutation: H24N
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 (E. coli) / References: UniProt: A5F686, peptidyl-tRNA hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.33 Å3/Da / Density % sol: 47.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 100mM Sodium Citrate, 200mM 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: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.43→62.7 Å / Num. obs: 14570 / % possible obs: 95.7 % / Redundancy: 5.3 % / Net I/σ(I): 14.43
Reflection shellResolution: 2.45→2.54 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: 2.43→62.69 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.922 / SU B: 10.44 / SU ML: 0.228 / Cross valid method: THROUGHOUT / ESU R: 0.579 / ESU R Free: 0.292 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25006 749 5 %RANDOM
Rwork0.18496 ---
obs0.18817 14236 95.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.946 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å2-0 Å20 Å2
2--2.2 Å2-0 Å2
3----3.26 Å2
Refinement stepCycle: 1 / Resolution: 2.43→62.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2957 0 0 107 3064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193012
X-RAY DIFFRACTIONr_bond_other_d0.0010.022937
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.9734075
X-RAY DIFFRACTIONr_angle_other_deg0.78936742
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6715390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.71824.724127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.36815505
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8291516
X-RAY DIFFRACTIONr_chiral_restr0.0760.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213455
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02668
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_it2.6043.9251566
X-RAY DIFFRACTIONr_mcbond_other2.6053.9231565
X-RAY DIFFRACTIONr_mcangle_it4.0715.8771954
X-RAY DIFFRACTIONr_mcangle_other4.075.8791955
X-RAY DIFFRACTIONr_scbond_it2.8694.1831446
X-RAY DIFFRACTIONr_scbond_other2.8684.1851447
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6766.1512121
X-RAY DIFFRACTIONr_long_range_B_refined6.55730.9313383
X-RAY DIFFRACTIONr_long_range_B_other6.55530.9253371
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.433→2.496 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 52 -
Rwork0.292 940 -
obs--86.41 %

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