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- PDB-5ivp: Crystal structure of the Peptidyl-tRNA hydrolase from Vibrio chol... -

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Basic information

Entry
Database: PDB / ID: 5ivp
TitleCrystal structure of the Peptidyl-tRNA hydrolase from Vibrio cholerae in the C121 space group at pH 6.5
ComponentsPeptidyl-tRNA hydrolase
KeywordsHYDROLASE / Peptidyl-tRNA hydrolase / Vibrio cholerae / Space group C121 / pH 6.5
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: 2.01 Å
AuthorsShahid, S. / Kabra, A. / Pal, R.K. / Arora, A.
CitationJournal: To Be Published
Title: Crystal structure of the Peptidyl-tRNA hydrolase from Vibrio cholerae in the C121 space group at pH 6.5
Authors: Shahid, S. / Kabra, A. / Pal, R.K. / Arora, A.
History
DepositionMar 21, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 22, 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 1.2Oct 30, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9314
Polymers43,5522
Non-polymers3782
Water2,198122
1
A: Peptidyl-tRNA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9652
Polymers21,7761
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidyl-tRNA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9652
Polymers21,7761
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.861, 44.507, 108.231
Angle α, β, γ (deg.)90.00, 95.97, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-201-

FLC

21B-201-

FLC

31A-371-

HOH

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Components

#1: Protein Peptidyl-tRNA hydrolase / PTH


Mass: 21776.166 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) / Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q9KQ21, peptidyl-tRNA hydrolase
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.07 Å3/Da / Density % sol: 40.61 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium citrate 0.2 Ammonium acetate, 17.5 % Polyethylene glycol 4000 protein concentration 8 mg/ml

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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: Aug 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.01→107.7 Å / Num. obs: 22748 / % possible obs: 95.7 % / Redundancy: 6.3 % / Net I/σ(I): 32.5
Reflection shellResolution: 2.01→2.08 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: 2.01→107.64 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.945 / SU B: 8.921 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.178 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22443 1175 5.2 %RANDOM
Rwork0.16116 ---
obs0.1644 21569 95.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.248 Å2
Baniso -1Baniso -2Baniso -3
1--2.08 Å2-0 Å2-0.77 Å2
2--4.15 Å20 Å2
3----1.87 Å2
Refinement stepCycle: LAST / Resolution: 2.01→107.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2996 0 26 122 3144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193079
X-RAY DIFFRACTIONr_bond_other_d0.0020.023028
X-RAY DIFFRACTIONr_angle_refined_deg1.7371.9834157
X-RAY DIFFRACTIONr_angle_other_deg0.85636969
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1165389
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.27324.58131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.77315536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3221516
X-RAY DIFFRACTIONr_chiral_restr0.1030.2460
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213489
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02675
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_it2.4872.9611562
X-RAY DIFFRACTIONr_mcbond_other2.4872.9591561
X-RAY DIFFRACTIONr_mcangle_it3.3754.4141949
X-RAY DIFFRACTIONr_mcangle_other3.3754.4151950
X-RAY DIFFRACTIONr_scbond_it3.1713.3311516
X-RAY DIFFRACTIONr_scbond_other3.1723.3321514
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7274.8532207
X-RAY DIFFRACTIONr_long_range_B_refined6.27624.0423432
X-RAY DIFFRACTIONr_long_range_B_other6.26323.9223405
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.011→2.063 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 72 -
Rwork0.185 1452 -
obs--86.99 %
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)
10.7062-0.02270.2740.2509-0.24190.6470.03960.0448-0.0598-0.0311-0.01650.02680.02530.0204-0.02310.08740.0039-0.01540.0063-0.01870.084583.864844.4852149.1266
20.6723-0.44320.77250.3461-0.70971.6585-0.07550.01850.11730.0315-0.0085-0.06490.02610.02050.0840.11320.0436-0.04040.032-0.01540.037171.958763.6376122.0641
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 197
2X-RAY DIFFRACTION2B3 - 197

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