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- PDB-3nea: Crystal Structure of Peptidyl-tRNA hydrolase from Francisella tul... -

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Basic information

Entry
Database: PDB / ID: 3nea
TitleCrystal Structure of Peptidyl-tRNA hydrolase from Francisella tularensis
ComponentsPeptidyl-tRNA hydrolase
KeywordsHYDROLASE / peptidyl-tRNA
Function / homology
Function and homology information


peptidyl-tRNA hydrolase / peptidyl-tRNA hydrolase activity / protein quality control for misfolded or incompletely synthesized proteins / rescue of stalled cytosolic ribosome / tRNA binding / cytoplasm
Similarity search - Function
Peptidyl-tRNA hydrolase / Peptidyl-tRNA hydrolase signature 2. / 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 speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsLam, R. / McGrath, T.E. / Romanov, V. / Gothe, S.A. / Peddi, S.R. / Razumova, E. / Lipman, R.S. / Branstrom, A.A. / Chirgadze, N.Y.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Structure of Francisella tularensis peptidyl-tRNA hydrolase.
Authors: Clarke, T.E. / Romanov, V. / Lam, R. / Gothe, S.A. / Peddi, S.R. / Razumova, E.B. / Lipman, R.S. / Branstrom, A.A. / Chirgadze, N.Y.
History
DepositionJun 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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

Downloads & links

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Assembly

Deposited unit
A: Peptidyl-tRNA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1857
Polymers22,8391
Non-polymers3466
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.683, 93.043, 33.027
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Peptidyl-tRNA hydrolase / PTH


Mass: 22838.969 Da / Num. of mol.: 1 / Fragment: UNP Residues 1-188
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Gene: FTT_0680c, pth / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus RIPL / References: UniProt: Q5NGZ6, peptidyl-tRNA hydrolase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.04 Å3/Da / Density % sol: 39.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG3350, 0.2M MgCl2, 0.1M Bis-Tris pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
41
51
61
71
81
91
101
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 28, 2007 / Details: VariMax HR
RadiationMonochromator: VariMax HR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 9412 / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.14 / Χ2: 1.022 / Net I/σ(I): 6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.25-2.336.70.499061.031100
2.33-2.426.70.3829201.0022100
2.42-2.536.70.3679311.0433100
2.53-2.676.70.3028961.0444100
2.67-2.836.70.2479361.0395100
2.83-3.056.70.1819351.0476100
3.05-3.366.70.1229331.0397100
3.36-3.856.70.0929501.0248100
3.85-4.856.60.0659670.979100
4.85-506.10.06510380.9811099.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.43 Å31.13 Å
Translation2.43 Å31.13 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.5.0109refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PTH

2pth


Resolution: 2.25→33.03 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.894 / WRfactor Rfree: 0.21 / WRfactor Rwork: 0.163 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.62 / SU ML: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.32 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.248 438 4.7 %RANDOM
Rwork0.19 ---
obs0.193 9380 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 55.76 Å2 / Biso mean: 25.057 Å2 / Biso min: 10.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.25→33.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1450 0 21 51 1522
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221501
X-RAY DIFFRACTIONr_angle_refined_deg1.2911.9562019
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8635188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.20825.36269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.72815264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.475156
X-RAY DIFFRACTIONr_chiral_restr0.0880.2223
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211121
X-RAY DIFFRACTIONr_mcbond_it0.5751.5928
X-RAY DIFFRACTIONr_mcangle_it1.09621495
X-RAY DIFFRACTIONr_scbond_it1.7943573
X-RAY DIFFRACTIONr_scangle_it2.9164.5523
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.3080.305390.20463267399.703
2.308-2.3710.287270.216642669100
2.371-2.4390.316300.219586616100
2.439-2.5140.288280.206607635100
2.514-2.5960.226290.215567596100
2.596-2.6870.339200.203565585100
2.687-2.7870.256290.227544573100
2.787-2.90.451240.193521545100
2.9-3.0280.311230.181513536100
3.028-3.1750.205270.188463490100
3.175-3.3450.16180.179471489100
3.345-3.5450.248220.173432454100
3.545-3.7870.251240.187418442100
3.787-4.0860.248120.17396408100
4.086-4.4690.193250.161353378100
4.469-4.9850.201170.157328345100
4.985-5.7350.237150.204295310100
5.735-6.9710.209150.186259274100
6.971-9.6460.13890.165208217100
9.646-33.0270.20350.24214214899.324

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