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- PDB-5imb: Crystal structure of peptidyl-tRNA hydrolase mutant-N14D from Vib... -

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Basic information

Entry
Database: PDB / ID: 5imb
TitleCrystal structure of peptidyl-tRNA hydrolase mutant-N14D from Vibrio cholerae
ComponentsPeptidyl-tRNA hydrolase
KeywordsHYDROLASE / Peptidyl-tRNA hydrolase / N14D mutant / 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
Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 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 6, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 12, 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
Revision 1.4Oct 23, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)43,5222
Polymers43,5222
Non-polymers00
Water50428
1
A: Peptidyl-tRNA hydrolase


Theoretical massNumber of molelcules
Total (without water)21,7611
Polymers21,7611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidyl-tRNA hydrolase


Theoretical massNumber of molelcules
Total (without water)21,7611
Polymers21,7611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.617, 72.381, 123.852
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: 21761.152 Da / Num. of mol.: 2 / Mutation: N14D
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) / Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q9KQ21, peptidyl-tRNA hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.31 Å3/Da / Density % sol: 46.78 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 0.1M Sodium citrate, 0.2M Ammonium acetate, 27.5% 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 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 16047 / % possible obs: 98.3 % / Redundancy: 5.7 % / Net I/σ(I): 28.26
Reflection shellResolution: 2.4→2.49 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZXP

4zxp


Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.933 / SU B: 24.081 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R: 0.465 / ESU R Free: 0.285 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26188 804 5 %RANDOM
Rwork0.20011 ---
obs0.20299 15176 98.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 62.717 Å2
Baniso -1Baniso -2Baniso -3
1-4.33 Å20 Å20 Å2
2--0.28 Å20 Å2
3----4.61 Å2
Refinement stepCycle: 1 / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2965 0 0 28 2993
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193023
X-RAY DIFFRACTIONr_bond_other_d0.0020.022979
X-RAY DIFFRACTIONr_angle_refined_deg2.0221.9744083
X-RAY DIFFRACTIONr_angle_other_deg1.08936850
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2695387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.3424.453128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.91215523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7961516
X-RAY DIFFRACTIONr_chiral_restr0.1070.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213435
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02669
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_it3.4365.1351554
X-RAY DIFFRACTIONr_mcbond_other3.4265.1351553
X-RAY DIFFRACTIONr_mcangle_it5.0837.6931939
X-RAY DIFFRACTIONr_mcangle_other5.0837.6941940
X-RAY DIFFRACTIONr_scbond_it3.7675.531469
X-RAY DIFFRACTIONr_scbond_other3.7665.5321470
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8118.1232144
X-RAY DIFFRACTIONr_long_range_B_refined7.35139.7553158
X-RAY DIFFRACTIONr_long_range_B_other7.35139.7653159
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.402→2.464 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 53 -
Rwork0.343 913 -
obs--81.59 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4288-0.36940.14050.7171-0.15671.05860.03390.08650.05630.0305-0.0144-0.1159-0.0662-0.0353-0.01940.0406-0.00210.00850.14930.00170.0263-1.1039-5.2499-5.5013
20.55270.0831-0.16440.43390.32571.50910.0396-0.07940.0020.03790.0878-0.0710.02030.0891-0.12740.07260.0224-0.02760.1318-0.0490.0307-1.7652-1.889428.1453
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 196
2X-RAY DIFFRACTION2B3 - 197

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