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- PDB-5ekt: Crystal structure of mutant-K146A of peptidyl-tRNA hydrolase from... -

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Basic information

Entry
Database: PDB / ID: 5ekt
TitleCrystal structure of mutant-K146A of peptidyl-tRNA hydrolase from Vibrio cholerae at 1.63A resolution.
ComponentsPeptidyl-tRNA hydrolase
KeywordsHYDROLASE / Peptidyl-tRNA hydrolase / K146A 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
CITRATE ANION / Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsShahid, S. / Kabr, A. / Pal, R.K. / Arora, A.
CitationJournal: To be published
Title: Crystal structure of mutant-K146A of peptidyl-tRNA hydrolase from Vibrio cholerae at 1.63A resolution.
Authors: Shahid, S. / Kabra, A. / Pal, R.K. / Arora, A.
History
DepositionNov 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6253
Polymers43,4362
Non-polymers1891
Water6,900383
1
A: Peptidyl-tRNA hydrolase


Theoretical massNumber of molelcules
Total (without water)21,7181
Polymers21,7181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidyl-tRNA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9072
Polymers21,7181
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-9 kcal/mol
Surface area16870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.934, 74.295, 123.571
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 1 - 197 / Label seq-ID: 3 - 199

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Peptidyl-tRNA hydrolase / PTH


Mass: 21718.064 Da / Num. of mol.: 2 / Mutation: K146A
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: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsVal (2) was introduced due to cloning artifact.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM Sodium citrate (pH 8), 200mM Ammonium acetate, 20% PEG 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: Aug 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. obs: 46655 / % possible obs: 88.4 % / Redundancy: 5.6 % / Net I/σ(I): 32.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZXP

4zxp


Resolution: 1.63→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.843 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2281 2345 5.1 %RANDOM
Rwork0.18711 ---
obs0.18914 44043 88.01 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.066 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20 Å2
2--1.23 Å2-0 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 1.63→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3034 0 13 383 3430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193106
X-RAY DIFFRACTIONr_bond_other_d0.010.023086
X-RAY DIFFRACTIONr_angle_refined_deg1.971.984188
X-RAY DIFFRACTIONr_angle_other_deg1.65237108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7345392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.61624.545132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.13315552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0761516
X-RAY DIFFRACTIONr_chiral_restr0.1150.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213502
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02682
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_it2.1571.6641574
X-RAY DIFFRACTIONr_mcbond_other2.1521.6621573
X-RAY DIFFRACTIONr_mcangle_it2.9512.4911964
X-RAY DIFFRACTIONr_mcangle_other2.952.4931965
X-RAY DIFFRACTIONr_scbond_it3.5812.0541532
X-RAY DIFFRACTIONr_scbond_other3.5712.0531530
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9982.9332224
X-RAY DIFFRACTIONr_long_range_B_refined7.64515.9353808
X-RAY DIFFRACTIONr_long_range_B_other7.63715.9193804
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 23910 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.628→1.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 188 -
Rwork0.23 3663 -
obs--99.51 %
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)
11.20660.61660.22151.71920.89461.89120.0105-0.13520.1345-0.0013-0.0440.1478-0.1679-0.01070.03350.0310.00140.00530.0254-0.01580.0219-21.146-5.6225.848
21.0643-0.115-0.39391.6974-0.84772.39820.01730.12830.0423-0.0340.13930.1463-0.04-0.1943-0.15660.0434-0.0108-0.02440.0380.03230.0382-21.331-1.792-28.141
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 197
2X-RAY DIFFRACTION2B1 - 197

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