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

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Basic information

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


prenyltransferase activity / metabolic process
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 DIPHOSPHATE / IMIDAZOLE / PYROPHOSPHATE 2- / AmbP3
Similarity search - Component
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 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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)75,17412
Polymers73,9782
Non-polymers1,19610
Water13,565753
1
A: aromatic prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7018
Polymers36,9891
Non-polymers7137
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: aromatic prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4724
Polymers36,9891
Non-polymers4833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.684, 211.534, 82.531
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
11B-761-

HOH

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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 , 6 types, 763 molecules

#2: Chemical ChemComp-8XL / 3-[(Z)-2-isocyanoethenyl]-1H-indole


Mass: 168.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H8N2
#3: Chemical
ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H5N2
#4: 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
#5: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#6: Chemical ChemComp-DMA / DIMETHYLALLYL DIPHOSPHATE / Dimethylallyl pyrophosphate


Mass: 246.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O7P2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 753 / 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: 56.14 % / Mosaicity: 0.486 °
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→25 Å / Num. obs: 90097 / % possible obs: 99.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.026 / Rrim(I) all: 0.052 / Χ2: 0.959 / Net I/σ(I): 15
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.763.90.4389310.8590.2510.4991.043100
1.76-1.833.90.31889440.9220.1850.3691.08299.9
1.83-1.913.90.24189180.9450.1410.281.15699.9
1.91-2.023.90.16389110.9750.0950.1890.96100
2.02-2.143.90.11889640.9840.0690.1370.92999.9
2.14-2.313.90.09589540.9880.0550.111.002100
2.31-2.543.90.05990040.9960.0340.0690.944100
2.54-2.913.90.04590520.9970.0260.0521.095100
2.91-3.663.90.02990920.9990.0170.0341.009100
3.66-253.80.0293270.9990.0110.0230.37799.6

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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: 0.983 / Cor.coef. Fo:Fc free: 0.968 / SU B: 3.576 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.075
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1662 4659 5.2 %RANDOM
Rwork0.1123 ---
obs0.1151 85469 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 136.03 Å2 / Biso mean: 26.176 Å2 / Biso min: 12.42 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20 Å20 Å2
2---0.01 Å20 Å2
3----1.01 Å2
Refinement stepCycle: final / Resolution: 1.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4858 0 80 753 5691
Biso mean--45.5 40.68 -
Num. residues----607
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195114
X-RAY DIFFRACTIONr_bond_other_d00.024612
X-RAY DIFFRACTIONr_angle_refined_deg1.4811.9546948
X-RAY DIFFRACTIONr_angle_other_deg0.783310712
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5325612
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61724.637248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.6815805
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2861520
X-RAY DIFFRACTIONr_chiral_restr0.1010.2744
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0215690
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021086
X-RAY DIFFRACTIONr_rigid_bond_restr6.57639726
X-RAY DIFFRACTIONr_sphericity_free30.2535477
X-RAY DIFFRACTIONr_sphericity_bonded16.05959869
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 331 -
Rwork0.167 6254 -
all-6585 -
obs--99.95 %

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