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- PDB-7w8x: DMSPP- and 6-Me-Trp-bound dimethylallyl tryptophan synthase, IptA -

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Basic information

Entry
Database: PDB / ID: 7w8x
TitleDMSPP- and 6-Me-Trp-bound dimethylallyl tryptophan synthase, IptA
Components6-dimethylallyltryptophan synthase
KeywordsTRANSFERASE / aromatic prenyltransferase / stpreptomyces / secondary metabolites
Function / homologyAromatic prenyltransferase, DMATS-type / Tryptophan dimethylallyltransferase / Aromatic prenyltransferase / transferase activity, transferring alkyl or aryl (other than methyl) groups / alkaloid metabolic process / Chem-8IK / DIMETHYLALLYL S-THIOLODIPHOSPHATE / 6-dimethylallyltryptophan synthase
Function and homology information
Biological speciesStreptomyces sp. SN-593 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSuemune, H. / Nagano, S. / Tomoya, H.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H04658 Japan
Japan Society for the Promotion of Science (JSPS)19H05780 Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Crystal structures of a 6-dimethylallyltryptophan synthase, IptA: Insights into substrate tolerance and enhancement of prenyltransferase activity.
Authors: Suemune, H. / Nishimura, D. / Mizutani, K. / Sato, Y. / Hino, T. / Takagi, H. / Shiozaki-Sato, Y. / Takahashi, S. / Nagano, S.
History
DepositionDec 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-dimethylallyltryptophan synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3034
Polymers39,7261
Non-polymers5763
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-8 kcal/mol
Surface area14310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.675, 44.742, 78.918
Angle α, β, γ (deg.)90.000, 96.934, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein 6-dimethylallyltryptophan synthase / Tryptophan 6-prenyltransferase


Mass: 39726.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. SN-593 (bacteria) / Gene: iptA, RVR_4274 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D6RT90
#2: Chemical ChemComp-DST / DIMETHYLALLYL S-THIOLODIPHOSPHATE / DMASPP / DMAPP / DMADP / Dimethylallyl pyrophosphate / dimethylallyl diphosphate / isoprenyl pyrophosphate


Mass: 262.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O6P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-8IK / (2S)-2-azanyl-3-(6-methyl-1H-indol-3-yl)propanoic acid


Mass: 218.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H14N2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.19 Å3/Da / Density % sol: 43.87 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: HEPEH pH7.0, Ammonium Sulfate

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Data collection

DiffractionMean temperature: 93.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→44.21 Å / Num. obs: 60703 / % possible obs: 98.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 23.11 Å2 / CC1/2: 0.988 / Net I/σ(I): 10.15
Reflection shellResolution: 1.45→1.5 Å / Num. unique obs: 5855 / CC1/2: 0.485

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7W8U

7w8u


Resolution: 1.45→44.21 Å / SU ML: 0.1946 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.3108
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2168 3044 5.03 %
Rwork0.19 57490 -
obs0.1913 60534 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.02 Å2
Refinement stepCycle: LAST / Resolution: 1.45→44.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2613 0 35 201 2849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00492714
X-RAY DIFFRACTIONf_angle_d0.80763713
X-RAY DIFFRACTIONf_chiral_restr0.0737418
X-RAY DIFFRACTIONf_plane_restr0.0056490
X-RAY DIFFRACTIONf_dihedral_angle_d23.5567965
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.3721450.33822502X-RAY DIFFRACTION95.73
1.47-1.50.30941280.30292548X-RAY DIFFRACTION96.33
1.5-1.520.2911300.26882595X-RAY DIFFRACTION98.95
1.52-1.550.26291280.25742608X-RAY DIFFRACTION97.78
1.55-1.580.28981280.24012565X-RAY DIFFRACTION99.26
1.58-1.610.26241550.23022593X-RAY DIFFRACTION98.14
1.61-1.650.23851430.21532574X-RAY DIFFRACTION98.8
1.65-1.690.23891250.20582598X-RAY DIFFRACTION98.95
1.69-1.730.23781420.20272620X-RAY DIFFRACTION98.5
1.73-1.770.22321500.20632596X-RAY DIFFRACTION99.56
1.77-1.830.25091510.20032585X-RAY DIFFRACTION99.02
1.83-1.890.22751200.19232637X-RAY DIFFRACTION99.1
1.89-1.950.20461330.19222631X-RAY DIFFRACTION99.28
1.95-2.030.2081310.18922638X-RAY DIFFRACTION99.64
2.03-2.120.25341360.19072628X-RAY DIFFRACTION99.39
2.12-2.240.19771530.18622619X-RAY DIFFRACTION99.35
2.24-2.380.23511340.19332660X-RAY DIFFRACTION99.68
2.38-2.560.2111490.19632610X-RAY DIFFRACTION99.39
2.56-2.820.22841370.19422644X-RAY DIFFRACTION99.36
2.82-3.220.22681440.18772633X-RAY DIFFRACTION99.04
3.22-4.060.19551350.16812685X-RAY DIFFRACTION99.54
4.06-44.210.18941470.17522721X-RAY DIFFRACTION98.83

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