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- PDB-4yzj: Crystal structure of selnomethionin-labeled indole prenyltransfer... -

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Basic information

Entry
Database: PDB / ID: 4yzj
TitleCrystal structure of selnomethionin-labeled indole prenyltransferase TleC
ComponentsTryptophan dimethylallyltransferase
KeywordsTRANSFERASE / indole prenyltransferase / PT-fold / indolactam V / teleocidins
Function / homologyAromatic prenyltransferase, DMATS-type / Tryptophan dimethylallyltransferase / transferase activity, transferring alkyl or aryl (other than methyl) groups / alkaloid metabolic process / Tryptophan dimethylallyltransferase
Function and homology information
Biological speciesStreptomyces blastmyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.106 Å
AuthorsMori, T. / Matsui, T. / Morita, H. / Abe, I.
CitationJournal: Nat Commun / Year: 2016
Title: Manipulation of prenylation reactions by structure-based engineering of bacterial indolactam prenyltransferases.
Authors: Mori, T. / Zhang, L. / Awakawa, T. / Hoshino, S. / Okada, M. / Morita, H. / Abe, I.
History
DepositionMar 25, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2Feb 5, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tryptophan dimethylallyltransferase


Theoretical massNumber of molelcules
Total (without water)43,6531
Polymers43,6531
Non-polymers00
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.870, 73.920, 110.420
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 Tryptophan dimethylallyltransferase


Mass: 43653.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces blastmyceticus (bacteria) / Gene: tleC / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A077K887
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100mM MES-NaOH (pH6.5), 1785mM (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 21, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.106→50 Å / Num. obs: 38054 / % possible obs: 99.4 % / Redundancy: 7.66 % / Net I/σ(I): 15.37

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XDSdata scaling
PHENIX(phenix.refine: 1.8.2_1309)phasing
RefinementMethod to determine structure: SAD / Resolution: 2.106→44.234 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 21.72 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2349 1021 5 %
Rwork0.1882 --
obs0.1905 20415 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.106→44.234 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2606 0 0 125 2731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092674
X-RAY DIFFRACTIONf_angle_d1.2113639
X-RAY DIFFRACTIONf_dihedral_angle_d13.376978
X-RAY DIFFRACTIONf_chiral_restr0.047386
X-RAY DIFFRACTIONf_plane_restr0.006487
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1063-2.21740.27211380.19652628X-RAY DIFFRACTION97
2.2174-2.35630.24641440.19932737X-RAY DIFFRACTION100
2.3563-2.53820.26451440.20072739X-RAY DIFFRACTION100
2.5382-2.79360.24861460.19922769X-RAY DIFFRACTION100
2.7936-3.19770.26011460.19542766X-RAY DIFFRACTION100
3.1977-4.02840.21181480.17332810X-RAY DIFFRACTION100
4.0284-44.24370.21821550.18522945X-RAY DIFFRACTION100

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