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- PDB-5ynw: Crystal structure of an aromatic prenyltransferase FAMD1 from Fis... -

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Basic information

Entry
Database: PDB / ID: 5ynw
TitleCrystal structure of an aromatic prenyltransferase FAMD1 from Fischerella ambigua UTEX 1903 in complex with DMASPP and INN
Componentsaromatic prenyltransferase
KeywordsTRANSFERASE / prenyltransferase
Function / homology
Function and homology information


hapalindole G dimethylallyltransferase / prenyltransferase activity
Similarity search - Function
Aromatic prenyltransferase, CloQ-type / Prenyltransferase-like superfamily / Aromatic prenyltransferase Orf2 / Aromatic prenyltransferase
Similarity search - Domain/homology
3-[(Z)-2-isocyanoethenyl]-1H-indole / DIMETHYLALLYL S-THIOLODIPHOSPHATE / IMIDAZOLE / Hapalindole dimethylallyltransferase
Similarity search - Component
Biological speciesFischerella ambigua UTEX 1903 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.95 Å
AuthorsWang, J. / Liu, W.D. / Chen, C.C. / Guo, R.T.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Structural insight into a novel indole prenyltransferase in hapalindole-type alkaloid biosynthesis.
Authors: Wang, J. / Chen, C.C. / Yang, Y. / Liu, W. / Ko, T.P. / Shang, N. / Hu, X. / Xie, Y. / Huang, J.W. / Zhang, Y. / Guo, R.T.
History
DepositionOct 25, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
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 2.1Mar 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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: aromatic prenyltransferase
B: aromatic prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8317
Polymers73,9782
Non-polymers8545
Water9,692538
1
A: aromatic prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3433
Polymers36,9891
Non-polymers3542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: aromatic prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4884
Polymers36,9891
Non-polymers4993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.583, 211.607, 82.421
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein aromatic prenyltransferase


Mass: 36988.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fischerella ambigua UTEX 1903 (bacteria)
Gene: ambP3 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: V5TDY7

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Non-polymers , 5 types, 543 molecules

#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-8XL / 3-[(Z)-2-isocyanoethenyl]-1H-indole


Mass: 168.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H8N2
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 538 / Source method: isolated from a natural source / Formula: H2O

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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: 2.8 Å3/Da / Density % sol: 56.09 % / Mosaicity: 1.255 °
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 1.0 M sodium citrate, 0.1 M Imidazole pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 8, 2017
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→25 Å / Num. obs: 57870 / % possible obs: 98.8 % / Redundancy: 5 % / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.057 / Rrim(I) all: 0.133 / Χ2: 1.094 / Net I/σ(I): 14.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.94-2.014.70.49556840.8410.2510.5581.15198.8
2.01-2.094.70.39557260.8870.20.4451.20898.6
2.09-2.184.70.32157250.9010.1620.3621.14898.7
2.18-2.34.70.26556880.9450.1330.2981.12498.3
2.3-2.444.80.23157200.9510.1140.2591.09498.2
2.44-2.6350.18957820.9580.0930.2121.02498.7
2.63-2.95.20.15758010.9710.0750.1751.04499.5
2.9-3.325.40.13658440.9760.0650.1521.04899.5
3.32-4.175.50.1158950.9820.0520.1221.04599.6
4.17-255.40.07660050.9910.0350.0841.08698

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
SOLVEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.95→25 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.189 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.123
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1942 2896 5 %RANDOM
Rwork0.151 ---
obs0.1532 54972 96.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 122.25 Å2 / Biso mean: 33.737 Å2 / Biso min: 18.38 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20 Å20 Å2
2---1.41 Å20 Å2
3---0.29 Å2
Refinement stepCycle: final / Resolution: 1.95→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4891 0 52 538 5481
Biso mean--53.71 43.59 -
Num. residues----613
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195107
X-RAY DIFFRACTIONr_bond_other_d0.0010.024606
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.9476949
X-RAY DIFFRACTIONr_angle_other_deg0.802310706
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0945615
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9624.64250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.16515807
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8911520
X-RAY DIFFRACTIONr_chiral_restr0.1010.2746
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0215689
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021067
LS refinement shellResolution: 1.953→2.003 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 154 -
Rwork0.209 3048 -
all-3202 -
obs--73.63 %

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