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- PDB-3v2i: Structure of a Peptidyl-tRNA hydrolase (PTH) from Burkholderia th... -

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Basic information

Entry
Database: PDB / ID: 3v2i
TitleStructure of a Peptidyl-tRNA hydrolase (PTH) from Burkholderia thailandensis
ComponentsPeptidyl-tRNA hydrolase
KeywordsHYDROLASE / SSGCID / Seattle Structural Genomics Center for Infectious Disease / RNA / Peptidyl-tRNA hydrolase
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
CITRIC ACID / Unknown ligand / Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesBurkholderia thailandensis E264 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionDec 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Database references
Revision 1.2Sep 13, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-tRNA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6173
Polymers24,4251
Non-polymers1922
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.340, 93.580, 106.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-359-

HOH

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Components

#1: Protein Peptidyl-tRNA hydrolase / PTH


Mass: 24424.916 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis E264 (bacteria)
Strain: BTH_I0472 / Gene: pth, BTH_I0472 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2T1B9, peptidyl-tRNA hydrolase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O

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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: 2.73 Å3/Da / Density % sol: 54.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: ButhA.17877.a.A1 PS01195 34.03 mg/ml, 1000mM sodium citrate, 100mM cacodylate pH 6.5. 25% ethylene glycol for cryoprotection. , VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 17, 2011
RadiationMonochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 32529 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 26.89 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 30.89
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.65-1.690.4224.89175052386100
1.69-1.740.3536.33184462292100
1.74-1.790.2738.11182512260100
1.79-1.840.21410.08178952213100
1.84-1.910.16612.73172112130100
1.91-1.970.12416.58164462040100
1.97-2.050.09620.92161521994100
2.05-2.130.07525.95154941914100
2.13-2.220.06330.2814969185699.9
2.22-2.330.05534.21140281743100
2.33-2.460.04639.16134691678100
2.46-2.610.04143.45129071615100
2.61-2.790.03748.9811768147999.9
2.79-3.010.03254.42109961406100
3.01-3.30.02863.13100561298100
3.3-3.690.02667.8189771180100
3.69-4.260.02471.857713104699.9
4.26-5.220.01975.466862896100
5.22-7.380.01872.635508713100
7.380.01472.97274739091.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å18.96 Å
Translation2.5 Å18.96 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OFV

3ofv


Resolution: 1.65→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.2 / WRfactor Rwork: 0.1719 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.8945 / SU B: 2.54 / SU ML: 0.045 / SU R Cruickshank DPI: 0.0774 / SU Rfree: 0.0804 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES: WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2055 1647 5.1 %RANDOM
Rwork0.1752 ---
obs0.1767 32529 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 49.82 Å2 / Biso mean: 21.2672 Å2 / Biso min: 10.69 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å20 Å2
2--0.42 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1439 0 14 202 1655
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191506
X-RAY DIFFRACTIONr_bond_other_d0.0010.021026
X-RAY DIFFRACTIONr_angle_refined_deg1.6051.9752045
X-RAY DIFFRACTIONr_angle_other_deg0.88532504
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7945193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.13523.48566
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.63315253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6571511
X-RAY DIFFRACTIONr_chiral_restr0.1680.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211686
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02301
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 114 -
Rwork0.226 2117 -
all-2231 -
obs--99.87 %
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)
11.59470.39090.79781.5583-0.0851.69250.01860.0963-0.0912-0.03820.0038-0.03230.11590.0825-0.02250.05580.01280.01230.05340.02470.062816.815511.300534.477
23.77582.5465-0.53853.6562-1.45381.3738-0.10440.484-0.1787-0.39150.1143-0.08220.21590.0552-0.00990.1011-0.00020.01180.1092-0.0070.0712.494510.81522.4184
31.1468-0.03670.57420.9991-0.45881.30980.0076-0.08830.07550.11920.0058-0.0165-0.0841-0.0659-0.01340.04010.00820.00820.04070.01530.062112.578116.955540.1106
43.49281.0842.58679.6564.53973.83160.0726-0.18520.28670.7372-0.2690.26670.2195-0.45470.19640.1624-0.00060.0280.17670.02360.138-2.876.838138.0613
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 35
2X-RAY DIFFRACTION2A36 - 60
3X-RAY DIFFRACTION3A61 - 183
4X-RAY DIFFRACTION4A184 - 196

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