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- PDB-6vy9: Crystal structure of NotF prenyltransferase -

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Basic information

Entry
Database: PDB / ID: 6vy9
TitleCrystal structure of NotF prenyltransferase
ComponentsDeoxybrevianamide E synthase notF
KeywordsTRANSFERASE / Fungal indole prenyltransferase
Function / homologybrevianamide F prenyltransferase (deoxybrevianamide E-forming) / Aromatic prenyltransferase DMATS-type, fungi / Aromatic prenyltransferase, DMATS-type / Tryptophan dimethylallyltransferase / Aromatic prenyltransferase / alkaloid metabolic process / prenyltransferase activity / Deoxybrevianamide E synthase notF
Function and homology information
Biological speciesAspergillus sp. (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 Å
AuthorsDan, Q. / Smith, J.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK042303 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Data Science-Driven Analysis of Substrate-Permissive Diketopiperazine Reverse Prenyltransferase NotF: Applications in Protein Engineering and Cascade Biocatalytic Synthesis of (-)-Eurotiumin A.
Authors: Kelly, S.P. / Shende, V.V. / Flynn, A.R. / Dan, Q. / Ye, Y. / Smith, J.L. / Tsukamoto, S. / Sigman, M.S. / Sherman, D.H.
History
DepositionFeb 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Deoxybrevianamide E synthase notF
B: Deoxybrevianamide E synthase notF
G: Deoxybrevianamide E synthase notF
H: Deoxybrevianamide E synthase notF
F: Deoxybrevianamide E synthase notF
D: Deoxybrevianamide E synthase notF
E: Deoxybrevianamide E synthase notF
C: Deoxybrevianamide E synthase notF


Theoretical massNumber of molelcules
Total (without water)430,6588
Polymers430,6588
Non-polymers00
Water0
1
A: Deoxybrevianamide E synthase notF
G: Deoxybrevianamide E synthase notF
D: Deoxybrevianamide E synthase notF
E: Deoxybrevianamide E synthase notF


Theoretical massNumber of molelcules
Total (without water)215,3294
Polymers215,3294
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9530 Å2
ΔGint-47 kcal/mol
Surface area62060 Å2
MethodPISA
2
B: Deoxybrevianamide E synthase notF
H: Deoxybrevianamide E synthase notF
F: Deoxybrevianamide E synthase notF
C: Deoxybrevianamide E synthase notF


Theoretical massNumber of molelcules
Total (without water)215,3294
Polymers215,3294
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9670 Å2
ΔGint-47 kcal/mol
Surface area61960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.591, 208.295, 217.374
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER

Dom-IDComponent-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUchain 'A'AA31 - 32951 - 349
12SERSERchain 'A'AA351 - 445371 - 465
21GLUGLUchain 'B'BB31 - 32951 - 349
22SERSERchain 'B'BB351 - 445371 - 465
31GLUGLUchain 'C'CH31 - 32951 - 349
32SERSERchain 'C'CH351 - 445371 - 465
41GLUGLUchain 'D'DF31 - 32951 - 349
42SERSERchain 'D'DF351 - 445371 - 465
51GLUGLUchain 'E'EG31 - 32951 - 349
52SERSERchain 'E'EG351 - 445371 - 465
61GLUGLUchain 'F'FE31 - 32951 - 349
62SERSERchain 'F'FE351 - 445371 - 465
71GLUGLUchain 'G'GC31 - 32951 - 349
72SERSERchain 'G'GC351 - 445371 - 465
81GLUGLUchain 'H'HD31 - 32951 - 349
82SERSERchain 'H'HD351 - 445371 - 465

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Components

#1: Protein
Deoxybrevianamide E synthase notF / Reverse prenyltransferase notF


Mass: 53832.211 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus sp. (mold) / Strain: MF297-2 / Gene: notF / Production host: Escherichia coli (E. coli)
References: UniProt: E0Y3X1, brevianamide F prenyltransferase (deoxybrevianamide E-forming)

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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: 4.04 Å3/Da / Density % sol: 69.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.7
Details: 3.0 M NaCl, 60 mM urea, 0.1 M MES pH 6.7, 15% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 13, 2019
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.19→49.32 Å / Num. obs: 115959 / % possible obs: 93.6 % / Redundancy: 7.5 % / Biso Wilson estimate: 81.48 Å2 / CC1/2: 1 / Net I/σ(I): 9.8
Reflection shellResolution: 3.19→3.3 Å / Num. unique obs: 11141 / CC1/2: 0.44

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LD7

4ld7


Resolution: 3.19→49.32 Å / SU ML: 0.5341 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 40.1832
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3158 1902 1.74 %
Rwork0.3072 107115 -
obs0.3074 109017 93.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 102.56 Å2
Refinement stepCycle: LAST / Resolution: 3.19→49.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25720 0 0 0 25720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008326552
X-RAY DIFFRACTIONf_angle_d1.171936112
X-RAY DIFFRACTIONf_chiral_restr0.05813736
X-RAY DIFFRACTIONf_plane_restr0.00884680
X-RAY DIFFRACTIONf_dihedral_angle_d16.21083448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.19-3.270.49631040.52386239X-RAY DIFFRACTION76.95
3.27-3.350.49641360.47137012X-RAY DIFFRACTION86.76
3.36-3.450.45151280.43447125X-RAY DIFFRACTION87.92
3.45-3.570.42261220.38897284X-RAY DIFFRACTION89.92
3.57-3.690.38571300.37177449X-RAY DIFFRACTION91.53
3.69-3.840.33721360.36547517X-RAY DIFFRACTION92.33
3.84-4.010.3961350.33517665X-RAY DIFFRACTION94.21
4.02-4.230.32261480.30297772X-RAY DIFFRACTION95.41
4.23-4.490.28091290.29067894X-RAY DIFFRACTION96.99
4.49-4.840.29811450.2748055X-RAY DIFFRACTION98.04
4.84-5.320.28531460.25478100X-RAY DIFFRACTION98.81
5.32-6.090.2941450.27728163X-RAY DIFFRACTION99.08
6.09-7.670.29341440.29268305X-RAY DIFFRACTION99.68
7.67-49.320.23521540.24128535X-RAY DIFFRACTION99.51

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