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- PDB-7e5t: Crystal structure of Fsa2 -

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Basic information

Entry
Database: PDB / ID: 7e5t
TitleCrystal structure of Fsa2
ComponentsDiels-Alderase fsa2
KeywordsBIOSYNTHETIC PROTEIN / Cyclase / diels-alderase / diels alder / [4+2] cycloaddition
Function / homologyDiels-Alderase, C-terminal domain / Isomerases; Intramolecular lyases / isomerase activity / ETHANOL / TRIETHYLENE GLYCOL / Diels-Alderase fsa2
Function and homology information
Biological speciesFusarium sp. (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1697752983 Å
AuthorsFujiyama, K. / Kato, N. / Kinugasa, K. / Hino, T. / Takahashi, S. / Nagano, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H04665 Japan
Japan Society for the Promotion of Science (JSPS)19H05780 Japan
Japan Society for the Promotion of Science (JSPS)19H04658 Japan
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Molecular Basis for Two Stereoselective Diels-Alderases that Produce Decalin Skeletons*.
Authors: Fujiyama, K. / Kato, N. / Re, S. / Kinugasa, K. / Watanabe, K. / Takita, R. / Nogawa, T. / Hino, T. / Osada, H. / Sugita, Y. / Takahashi, S. / Nagano, S.
History
DepositionFeb 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 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: Diels-Alderase fsa2
B: Diels-Alderase fsa2
C: Diels-Alderase fsa2
D: Diels-Alderase fsa2
E: Diels-Alderase fsa2
F: Diels-Alderase fsa2
G: Diels-Alderase fsa2
H: Diels-Alderase fsa2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)336,97818
Polymers336,2218
Non-polymers75710
Water22,0861226
1
A: Diels-Alderase fsa2


Theoretical massNumber of molelcules
Total (without water)42,0281
Polymers42,0281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Diels-Alderase fsa2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0742
Polymers42,0281
Non-polymers461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Diels-Alderase fsa2


Theoretical massNumber of molelcules
Total (without water)42,0281
Polymers42,0281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Diels-Alderase fsa2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1664
Polymers42,0281
Non-polymers1383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Diels-Alderase fsa2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0742
Polymers42,0281
Non-polymers461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Diels-Alderase fsa2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1782
Polymers42,0281
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Diels-Alderase fsa2


Theoretical massNumber of molelcules
Total (without water)42,0281
Polymers42,0281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Diels-Alderase fsa2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4045
Polymers42,0281
Non-polymers3764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.929, 80.229, 135.159
Angle α, β, γ (deg.)90.000, 108.533, 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
Diels-Alderase fsa2 / Fusarisetin A biosynthesis protein 2


Mass: 42027.648 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium sp. (strain FN080326) (fungus)
Gene: fsa2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0E4AYE7, Isomerases; Intramolecular lyases
#2: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1226 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.05 Å3/Da / Density % sol: 39.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 26-29% (v/v) polyethylene glycol 3350, 0.10M Bis-Tris HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.16977→45.0444 Å / Num. obs: 141327 / % possible obs: 97.61 % / Redundancy: 3.5 % / Biso Wilson estimate: 29.0333207286 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.109 / Net I/σ(I): 8.48
Reflection shellResolution: 2.17→2.248 Å / Num. unique obs: 13856 / CC1/2: 0.78

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
pointless1.11.6data scaling
Aimless0.5.32data scaling
PHASER2.7.17phasing
Coot0.8.9.2model building
PHENIX1.11.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Phm7

Resolution: 2.1697752983→45.0443856263 Å / SU ML: 0.274703588188 / Cross valid method: FREE R-VALUE / σ(F): 1.36056709229 / Phase error: 24.075131165
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.235222273643 7265 5.16809651856 %
Rwork0.179790258307 133309 -
obs0.182641334888 140574 97.6269350168 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.2130249912 Å2
Refinement stepCycle: LAST / Resolution: 2.1697752983→45.0443856263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22889 0 50 1226 24165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044553968349323500
X-RAY DIFFRACTIONf_angle_d0.70017598049231919
X-RAY DIFFRACTIONf_chiral_restr0.05192354664213486
X-RAY DIFFRACTIONf_plane_restr0.004129215338014160
X-RAY DIFFRACTIONf_dihedral_angle_d18.414964527813763
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1698-2.19440.2791727164212520.2353413879074332X-RAY DIFFRACTION97.056955325
2.1944-2.22020.3163339263372520.2376851416864405X-RAY DIFFRACTION96.8191268191
2.2202-2.24730.2656007469792360.221902102374385X-RAY DIFFRACTION97.0390592188
2.2473-2.27580.3019198619011870.2161733045954458X-RAY DIFFRACTION97.0133667502
2.2758-2.30570.2760325672142070.2179813898544416X-RAY DIFFRACTION97.3263157895
2.3057-2.33730.2775190712062080.2230506394174452X-RAY DIFFRACTION97.0631118517
2.3373-2.37070.2925864209372340.231590031934380X-RAY DIFFRACTION97.1368421053
2.3707-2.40610.3012769114962660.2236883354314349X-RAY DIFFRACTION97.2602739726
2.4061-2.44370.3243915379932360.2231310917954444X-RAY DIFFRACTION97.5406419341
2.4437-2.48370.2782511276962150.2140320265434451X-RAY DIFFRACTION97.4926870038
2.4837-2.52650.2763549796912330.2081221679634436X-RAY DIFFRACTION97.6165586452
2.5265-2.57250.260099046992070.2141630148044428X-RAY DIFFRACTION97.3330533389
2.5725-2.6220.2738692414243160.2048496341244345X-RAY DIFFRACTION97.3272081854
2.622-2.67550.273943178212440.1930562820424458X-RAY DIFFRACTION97.8360382855
2.6755-2.73360.2661060218052670.1876132078774386X-RAY DIFFRACTION97.9372763629
2.7336-2.79720.258475064712950.1879742470054421X-RAY DIFFRACTION98.2295355134
2.7972-2.86720.2262256498152410.1881542656754449X-RAY DIFFRACTION98.0556136316
2.8672-2.94470.2658888718962460.1932673597474469X-RAY DIFFRACTION98.0045728539
2.9447-3.03130.2651520692132510.1968241209494449X-RAY DIFFRACTION98.3263598326
3.0313-3.12910.2573286576992650.1903765812914433X-RAY DIFFRACTION98.2023411371
3.1291-3.24090.2470753618272450.1780535681984449X-RAY DIFFRACTION98.2419422352
3.2409-3.37070.2180786161832170.1747046696364499X-RAY DIFFRACTION97.9642708766
3.3707-3.5240.2324918989822440.1785898300564464X-RAY DIFFRACTION97.35318445
3.524-3.70970.2344495999982700.1746601973354399X-RAY DIFFRACTION98.0264539156
3.7097-3.9420.2045736848332730.1587947800264478X-RAY DIFFRACTION97.9385693671
3.942-4.24620.1923408178582150.14565433644476X-RAY DIFFRACTION97.5057160673
4.2462-4.67310.1671296632352080.1325173895424503X-RAY DIFFRACTION97.1740924092
4.6731-5.34830.1881899213392480.1416214381874505X-RAY DIFFRACTION97.7380217972
5.3483-6.73470.2099748454012490.173033491394563X-RAY DIFFRACTION98.8496302383
6.7347-45.0440.1930547349342380.1696190029554627X-RAY DIFFRACTION97.5145319703

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