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- PDB-4yzk: Crystal structure of the indole prenyltransferase TleC apo structure -

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Basic information

Entry
Database: PDB / ID: 4yzk
TitleCrystal structure of the indole prenyltransferase TleC apo structure
ComponentsTryptophan dimethylallyltransferase
KeywordsTRANSFERASE / indole prenyltransferase / PT-fold / indolactam V
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 / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMori, 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 19, 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 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

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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)43,1841
Polymers43,1841
Non-polymers00
Water4,035224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.990, 74.060, 111.030
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: 43184.219 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 / References: UniProt: A0A077K887
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100mM MES (pH6.5), 1500mM (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 10, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 25886 / % possible obs: 99.5 % / Redundancy: 7.19 % / Net I/σ(I): 13.42

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YZJ

4yzj


Resolution: 1.95→44.421 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 22.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2316 1292 4.99 %
Rwork0.1863 --
obs0.1886 25878 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→44.421 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2652 0 0 224 2876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072720
X-RAY DIFFRACTIONf_angle_d1.0323699
X-RAY DIFFRACTIONf_dihedral_angle_d12.4961000
X-RAY DIFFRACTIONf_chiral_restr0.04392
X-RAY DIFFRACTIONf_plane_restr0.006495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9498-2.02790.29221360.22952585X-RAY DIFFRACTION96
2.0279-2.12020.27661430.21622704X-RAY DIFFRACTION100
2.1202-2.2320.24141410.19972692X-RAY DIFFRACTION100
2.232-2.37180.25181420.19432708X-RAY DIFFRACTION100
2.3718-2.55490.26481410.19762708X-RAY DIFFRACTION100
2.5549-2.8120.25881430.19682732X-RAY DIFFRACTION100
2.812-3.21880.23471460.19572769X-RAY DIFFRACTION100
3.2188-4.05490.20881460.16122766X-RAY DIFFRACTION100
4.0549-44.43210.21540.17492922X-RAY DIFFRACTION100

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