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- PDB-5ike: Crystal structure of mutant-D97N of peptidyl-tRNA hydrolase from ... -

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Basic information

Entry
Database: PDB / ID: 5ike
TitleCrystal structure of mutant-D97N of peptidyl-tRNA hydrolase from Vibrio cholerae
ComponentsPeptidyl-tRNA hydrolase
KeywordsHYDROLASE / Peptidyl-tRNA hydrolase / D97N mutant / Vibrio cholerae
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 O1 biovar El Tor str. N16961 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.09 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
DepositionMar 3, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 8, 2017Provider: 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 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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


Theoretical massNumber of molelcules
Total (without water)43,5502
Polymers43,5502
Non-polymers00
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-13 kcal/mol
Surface area16180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.455, 71.628, 123.929
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: 21775.182 Da / Num. of mol.: 2 / Mutation: D97N
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTEV protease site was present cleaved in the purification process

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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: 2.29 Å3/Da / Density % sol: 46.35 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 100 mM Sodium citrate, 200 mM 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 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 23401 / % possible obs: 97.3 % / Redundancy: 6.6 % / Net I/σ(I): 19.68
Reflection shellResolution: 2.1→2.14 Å

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Processing

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

4zxp


Resolution: 2.09→35.79 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.882 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25431 1201 5.1 %RANDOM
Rwork0.18298 ---
obs0.18645 22168 97.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.957 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å2-0 Å2-0 Å2
2--2.15 Å2-0 Å2
3----2.92 Å2
Refinement stepCycle: LAST / Resolution: 2.09→35.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2980 0 0 141 3121
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193045
X-RAY DIFFRACTIONr_bond_other_d0.0010.022996
X-RAY DIFFRACTIONr_angle_refined_deg1.7461.9724113
X-RAY DIFFRACTIONr_angle_other_deg0.85736885
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8355389
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.92524.58131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.3315526
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1181516
X-RAY DIFFRACTIONr_chiral_restr0.1010.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213469
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02679
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_it2.9143.4811562
X-RAY DIFFRACTIONr_mcbond_other2.9123.4781561
X-RAY DIFFRACTIONr_mcangle_it4.2215.1971949
X-RAY DIFFRACTIONr_mcangle_other4.2215.21950
X-RAY DIFFRACTIONr_scbond_it3.6443.8841483
X-RAY DIFFRACTIONr_scbond_other3.6383.8771481
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5635.6632164
X-RAY DIFFRACTIONr_long_range_B_refined7.66328.153476
X-RAY DIFFRACTIONr_long_range_B_other7.66728.053451
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.094→2.148 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 84 -
Rwork0.255 1513 -
obs--91.78 %

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