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- PDB-3i4x: Crystal structure of the dimethylallyl tryptophan synthase FgaPT2... -

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Basic information

Entry
Database: PDB / ID: 3i4x
TitleCrystal structure of the dimethylallyl tryptophan synthase FgaPT2 from Aspergillus fumigatus in complex with Trp and DMSPP
ComponentsTryptophan dimethylallyltransferase
KeywordsTRANSFERASE / prenyl transferase / dimethylallyl tryptophan synthase / PT barrel / tryptophan complex / Dimethylallyl S-thiolodiphosphate complex / Alkaloid metabolism
Function / homology
Function and homology information


4-dimethylallyltryptophan synthase / tryptophan dimethylallyltransferase activity / fumigaclavine C biosynthetic process / prenyltransferase activity
Similarity search - Function
Tryptophan dimethylallyltransferase / Aromatic prenyltransferase DMATS-type, fungi / Aromatic prenyltransferase, DMATS-type / Tryptophan dimethylallyltransferase / Aromatic prenyltransferase
Similarity search - Domain/homology
DIMETHYLALLYL S-THIOLODIPHOSPHATE / TRYPTOPHAN / Tryptophan dimethylallyltransferase
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSchall, C. / Zocher, G. / Stehle, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: The structure of dimethylallyl tryptophan synthase reveals a common architecture of aromatic prenyltransferases in fungi and bacteria
Authors: Metzger, U. / Schall, C. / Zocher, G. / Unsoeld, I. / Stec, E. / Li, S.-M. / Heide, L. / Stehle, T.
History
DepositionJul 3, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Oct 16, 2019Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / entity
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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: Tryptophan dimethylallyltransferase
B: Tryptophan dimethylallyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,1018
Polymers105,9842
Non-polymers1,1176
Water10,539585
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.070, 97.850, 125.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tryptophan dimethylallyltransferase / L-tryptophan dimethylallyl transferase / DMATS / All-trans-hexaprenyl-diphosphate synthase


Mass: 52992.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: Q50EL0, 4-dimethylallyltryptophan synthase
#2: Chemical ChemComp-DST / DIMETHYLALLYL S-THIOLODIPHOSPHATE / DMASPP / DMAPP / DMADP / Dimethylallyl pyrophosphate / dimethylallyl diphosphate / isoprenyl pyrophosphate


Mass: 262.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O6P2S
#3: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 585 / Source method: isolated from a natural source / Formula: H2O
Sequence details1. RESIDUE SER443ALA IS A NATURAL VARIENT IN STRAIN: B5233 / ATCC 13073 OF DMAW_ASPFU ...1. RESIDUE SER443ALA IS A NATURAL VARIENT IN STRAIN: B5233 / ATCC 13073 OF DMAW_ASPFU (UNIPROTKB/SWISS-PROT Q50EL0). 2. AUTHOR CANNOT CLARIFY RESIDUES A 452(GLY) TO 454(TYR) BELONG TO EITHER CHAIN A OR CHAIN B. RESIDUES A 452(GLY) TO 454(TYR) WERE ASSIGNED TO CHAIN A TEMPORARY.

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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: 2.28 Å3/Da / Density % sol: 46.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 26% 1,3-butanediol, 50mM sodium L-lactate, 100mM sodium MOPSO pH 7.0, 2mM DTT, vapour diffusion, hanging drop, temperature 277K, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.275 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 25, 2009
RadiationMonochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.275 Å / Relative weight: 1
ReflectionResolution: 2.08→24.94 Å / Num. all: 59038 / Num. obs: 58992 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 5.9 % / Biso Wilson estimate: 37.7 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.7
Reflection shellResolution: 2.08→2.13 Å / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 3.44 / Num. unique all: 58992 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.5.0070refinement
PDB_EXTRACT3.005data extraction
XDSdata scaling
XDSdata reduction
REFMAC5.5.0070phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3I4Z

3i4z


Resolution: 2.1→24.94 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 8.554 / SU ML: 0.104 / Cross valid method: THROUGHOUT R free / σ(F): 0 / σ(I): 3.44 / ESU R: 0.174 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1663 3 %RANDOM
Rwork0.149 ---
all0.15 55615 --
obs0.151 55615 100 %-
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: 86.28 Å2 / Biso mean: 32.424 Å2 / Biso min: 5.97 Å2
Baniso -1Baniso -2Baniso -3
1-1.91 Å20 Å20 Å2
2---0.97 Å20 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 2.1→24.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6871 0 70 585 7526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227192
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.9649800
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1975861
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.05622.73337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.945151180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0341559
X-RAY DIFFRACTIONr_chiral_restr0.1030.21067
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215509
X-RAY DIFFRACTIONr_mcbond_it1.69934288
X-RAY DIFFRACTIONr_mcangle_it2.55246957
X-RAY DIFFRACTIONr_scbond_it2.25732904
X-RAY DIFFRACTIONr_scangle_it3.11742835
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 125 -
Rwork0.17 4037 -
all-4162 -
obs--100 %
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)
10.4226-0.04030.04820.8191-0.13490.5655-0.0355-0.0294-0.02450.0144-0.00730.0137-0.0315-0.00310.04270.00470.00240.00020.21630.00480.193731.60480.95611.329
20.3036-0.1453-0.01920.92590.08250.460.02590.0277-0.01730-0.03690.01630.0143-0.03250.0110.02730.00120.01380.2038-0.00990.196213.16473.4547.062
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 425
2X-RAY DIFFRACTION2B3 - 423

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