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- PDB-8d7f: FlvF from Aspergillus flavus in complex with Bis-Tris -

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Basic information

Entry
Database: PDB / ID: 8d7f
TitleFlvF from Aspergillus flavus in complex with Bis-Tris
ComponentsTerpene cyclase flvF
KeywordsLYASE / fungal protein / terpene cyclase fold / C-N bond formation
Function / homologyLyases; Carbon-oxygen lyases; Acting on phosphates / terpenoid biosynthetic process / Isoprenoid synthase domain superfamily / lyase activity / metal ion binding / Terpene cyclase flvF
Function and homology information
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsTararina, M.A. / Christianson, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM056838 United States
CitationJournal: Biochemistry / Year: 2022
Title: Structure of the Repurposed Fungal Terpene Cyclase FlvF Implicated in the C-N Bond-Forming Reaction of Flavunoidine Biosynthesis.
Authors: Tararina, M.A. / Yee, D.A. / Tang, Y. / Christianson, D.W.
History
DepositionJun 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Terpene cyclase flvF
B: Terpene cyclase flvF
C: Terpene cyclase flvF
D: Terpene cyclase flvF
E: Terpene cyclase flvF
F: Terpene cyclase flvF
G: Terpene cyclase flvF
H: Terpene cyclase flvF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)342,08821
Polymers340,3058
Non-polymers1,78313
Water00
1
A: Terpene cyclase flvF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0494
Polymers42,5381
Non-polymers5113
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Terpene cyclase flvF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0494
Polymers42,5381
Non-polymers5113
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Terpene cyclase flvF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6302
Polymers42,5381
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Terpene cyclase flvF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8393
Polymers42,5381
Non-polymers3012
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Terpene cyclase flvF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6302
Polymers42,5381
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Terpene cyclase flvF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6302
Polymers42,5381
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Terpene cyclase flvF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6302
Polymers42,5381
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Terpene cyclase flvF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6302
Polymers42,5381
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.650, 194.999, 101.370
Angle α, β, γ (deg.)90.000, 106.190, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Terpene cyclase flvF / Flavunoidine biosynthesis cluster protein F


Mass: 42538.148 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus flavus (strain ATCC 200026 / FGSC A1120 / IAM 13836 / NRRL 3357 / JCM 12722 / SRRC 167) (mold)
Strain: ATCC 200026 / FGSC A1120 / IAM 13836 / NRRL 3357 / JCM 12722 / SRRC 167
Gene: flvF, AFLA_135460 / Plasmid: pET His6 GFP TEV LIC / Details (production host): Addgene #29663 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: B8NHE1, Lyases; Carbon-oxygen lyases; Acting on phosphates
#2: Chemical
ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H19NO5 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
Has ligand of interestY

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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: 2.54 Å3/Da / Density % sol: 52 %
Description: plates approximately 0.1 x 0.1 x 0.01 mm dimension
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 200 mM magnesium chloride hexahydrate, 100 mM Bis-Tris pH 6.5, 25% PEG 3350, 10 mM yttrium(III) chloride hexahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2021
RadiationMonochromator: MD2 diffractometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.62→97.35 Å / Num. obs: 99760 / % possible obs: 98.9 % / Redundancy: 2 % / Biso Wilson estimate: 39.39 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.032 / Net I/σ(I): 18.7
Reflection shellResolution: 2.62→2.72 Å / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 9.4 / Num. unique obs: 9657 / CC1/2: 0.474 / Rpim(I) all: 0.096 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MOSFLM7.4.0data reduction
Aimlessdata scaling
PHASER1.20.1-4487-000phasing
Coot1.0.0model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2 model 1c37a

Resolution: 2.62→97.35 Å / SU ML: 0.3636 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.4787
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2426 2000 2.01 %
Rwork0.2084 97691 -
obs0.2091 99691 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.29 Å2
Refinement stepCycle: LAST / Resolution: 2.62→97.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22160 0 118 0 22278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006522905
X-RAY DIFFRACTIONf_angle_d1.168531110
X-RAY DIFFRACTIONf_chiral_restr0.06083239
X-RAY DIFFRACTIONf_plane_restr0.00774010
X-RAY DIFFRACTIONf_dihedral_angle_d17.5248281
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.62-2.690.31451350.2776578X-RAY DIFFRACTION92.85
2.69-2.760.31251440.26696993X-RAY DIFFRACTION99.39
2.76-2.840.32131420.26687015X-RAY DIFFRACTION99.35
2.84-2.930.35741430.27296970X-RAY DIFFRACTION99.21
2.93-3.040.34161430.25656972X-RAY DIFFRACTION99.15
3.04-3.160.25181440.23956985X-RAY DIFFRACTION99.11
3.16-3.30.3011400.23736909X-RAY DIFFRACTION97.73
3.3-3.480.28531460.22187065X-RAY DIFFRACTION99.85
3.48-3.70.24371430.20837016X-RAY DIFFRACTION99.9
3.7-3.980.23151440.18557075X-RAY DIFFRACTION99.72
3.98-4.380.1981440.1696999X-RAY DIFFRACTION99.15
4.38-5.020.17891420.17046959X-RAY DIFFRACTION98.43
5.02-6.320.23931450.20467080X-RAY DIFFRACTION99.85
6.32-97.350.17131450.17467075X-RAY DIFFRACTION98.84

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