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- PDB-3i4z: Crystal structure of the dimethylallyl tryptophan synthase FgaPT2... -

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Basic information

Entry
Database: PDB / ID: 3i4z
TitleCrystal structure of the dimethylallyl tryptophan synthase FgaPT2 from Aspergillus fumigatus
ComponentsTryptophan dimethylallyltransferase
KeywordsTRANSFERASE / prenyl transferase / PT barrel / 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
1,3-BUTANEDIOL / Tryptophan dimethylallyltransferase
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 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 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Tryptophan dimethylallyltransferase
B: Tryptophan dimethylallyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,07414
Polymers105,9842
Non-polymers1,08912
Water12,286682
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint26 kcal/mol
Surface area34010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.060, 98.790, 125.630
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-BU2 / 1,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 682 / 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 446(PRO) TO 458(LEU) BELONG TO EITHER CHAIN A OR CHAIN B. RESIDUES A 446(PRO) TO 458(LEU) 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: 2

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.52 %
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
IDMean temperature (K)Crystal-ID
11031
21031
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONESRF ID14-410.9395
ROTATING ANODERIGAKU MICROMAX-007 HF21.541789
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDNov 15, 2008
MAR scanner 345 mm plate2IMAGE PLATEDec 23, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal, Si(111) or Si(311)SINGLE WAVELENGTHMx-ray1
2Cu K alphaSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.93951
21.5417891
ReflectionNumber: 536343 / Rmerge(I) obs: 0.134 / D res high: 2.7 Å / Num. obs: 52137 / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
12.0824.7141770.410.038
8.5412.08107310010.039
6.978.54138310010.055
6.046.97165310010.075
5.46.04185110010.085
4.935.4205010010.073
4.574.93226310010.072
4.274.57239610010.074
4.034.27256810010.086
3.824.03271310010.101
3.643.82282510010.115
3.493.64299110010.132
3.353.49313010010.165
3.233.35321710010.197
3.123.23336610010.241
3.023.12344910010.314
2.933.02359810010.355
2.852.93368110010.394
2.772.85376710010.466
2.72.77374697.210.573
ReflectionResolution: 1.76→24.71 Å / Num. obs: 98932 / % possible obs: 98.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 29.8 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 14.14
Reflection shellResolution: 1.76→1.81 Å / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.2 / % possible all: 91.3

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SHARPphasing
DMphasing
REFMAC5.5.0070refinement
PDB_EXTRACT3.005data extraction
XDSdata scaling
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.76→24.71 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 4.333 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.183 2471 2.5 %RANDOM
Rwork0.151 ---
all0.151 98911 --
obs0.152 98911 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.49 Å2 / Biso mean: 26.02 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-2.23 Å20 Å20 Å2
2---0.66 Å20 Å2
3----1.57 Å2
Refinement stepCycle: LAST / Resolution: 1.76→24.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6950 0 72 682 7704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227557
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.96610348
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7455963
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.95122.825354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.614151265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8461562
X-RAY DIFFRACTIONr_chiral_restr0.1030.21140
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215816
X-RAY DIFFRACTIONr_mcbond_it2.26264487
X-RAY DIFFRACTIONr_mcangle_it3.27777342
X-RAY DIFFRACTIONr_scbond_it3.62273070
X-RAY DIFFRACTIONr_scangle_it4.88172956
LS refinement shellResolution: 1.76→1.805 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 175 -
Rwork0.226 6809 -
all-6984 -
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)
10.52150.02160.0560.6343-0.2250.8027-0.02940.0189-0.04280.0191-0.0033-0.0042-0.00160.00710.03270.00730.0050.00510.2187-0.0040.261531.60480.95611.329
20.5403-0.2579-0.08181.11390.33830.98910.00140.0088-0.1010.0589-0.05840.09950.1551-0.13510.05710.0455-0.02180.0360.205-0.0080.278113.16473.4547.062
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 425
2X-RAY DIFFRACTION2B3 - 423

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