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

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Basic information

Entry
Database: PDB / ID: 5ynv
TitleCrystal structure of an aromatic prenyltransferase FAMD1 from Fischerella ambigua UTEX 1903 in complex with DMASPP
Componentsaromatic prenyltransferase
KeywordsTRANSFERASE / prenyltransferase
Function / homologyAromatic prenyltransferase, CloQ-type / Prenyltransferase-like superfamily / Aromatic prenyltransferase Orf2 / Aromatic prenyltransferase / prenyltransferase activity / metabolic process / DIMETHYLALLYL S-THIOLODIPHOSPHATE / AmbP3
Function and homology information
Biological speciesFischerella ambigua UTEX 1903 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.7 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)74,5945
Polymers73,9782
Non-polymers6163
Water13,457747
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)37,2512
Polymers36,9891
Non-polymers2621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.917, 211.420, 82.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-793-

HOH

21A-819-

HOH

31B-711-

HOH

41B-737-

HOH

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Components

#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
#2: Chemical ChemComp-DST / DIMETHYLALLYL S-THIOLODIPHOSPHATE / DMASPP / DMAPP / DMADP / Dimethylallyl pyrophosphate / dimethylallyl diphosphate / isoprenyl pyrophosphate / Dimethylallyl pyrophosphate


Mass: 262.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O6P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 747 / 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: 2.81 Å3/Da / Density % sol: 56.26 % / Mosaicity: 0.46 °
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: 1.7→50 Å / Num. obs: 90773 / % possible obs: 99.9 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.027 / Rrim(I) all: 0.058 / Χ2: 0.712 / Net I/σ(I): 15.3 / Num. measured all: 440723
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.764.80.33689660.9240.1720.3781.0899.7
1.76-1.834.80.24689800.960.1250.2771.031100
1.83-1.914.80.1889960.9740.0920.2030.949100
1.91-2.024.90.12990220.9870.0660.1450.864100
2.02-2.144.90.09890260.9910.050.110.762100
2.14-2.314.90.09190360.990.0460.1030.795100
2.31-2.544.90.06890720.9950.0340.0770.616100
2.54-2.914.90.0591110.9970.0260.0570.446100
2.91-3.664.90.04991680.9970.0250.0550.449100
3.66-504.70.02893960.9990.0150.0320.15699.6

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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: 1.7→25 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.965 / SU B: 3.168 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.076 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1709 4670 5.2 %RANDOM
Rwork0.1148 ---
obs0.1177 85679 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 157.4 Å2 / Biso mean: 26.238 Å2 / Biso min: 10.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å2-0 Å2
2---0.51 Å20 Å2
3----0.31 Å2
Refinement stepCycle: final / Resolution: 1.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4901 0 34 747 5682
Biso mean--34.92 39.69 -
Num. residues----614
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0195081
X-RAY DIFFRACTIONr_angle_refined_deg1.451.9456912
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7365614
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.98224.637248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.98715810
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1041520
X-RAY DIFFRACTIONr_chiral_restr0.1210.2746
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.0213931
X-RAY DIFFRACTIONr_rigid_bond_restr8.70835081
X-RAY DIFFRACTIONr_sphericity_free30.1015506
X-RAY DIFFRACTIONr_sphericity_bonded21.87255188
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 327 -
Rwork0.164 6277 -
all-6604 -
obs--100 %

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