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- PDB-7f14: Crystal structure of isomerase Dcr3 complex with substrate analogue 3 -

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Basic information

Entry
Database: PDB / ID: 7f14
TitleCrystal structure of isomerase Dcr3 complex with substrate analogue 3
ComponentsDcr3
KeywordsISOMERASE / tetrahydroxanthones / blennolides
Function / homologyChem-0BJ
Function and homology information
Biological speciesDiaporthe longicolla (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsYang, J. / Mori, T. / Abe, I.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Structural Basis for Isomerization Reactions in Fungal Tetrahydroxanthone Biosynthesis and Diversification.
Authors: Yang, J. / Mori, T. / Wei, X. / Matsuda, Y. / Abe, I.
History
DepositionJun 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Dcr3
B: Dcr3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8454
Polymers39,2402
Non-polymers6052
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-15 kcal/mol
Surface area14150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.094, 104.094, 138.681
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2

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Components

#1: Protein Dcr3


Mass: 19620.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Diaporthe longicolla (fungus) / Strain: TWH P74 / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-0BJ / methyl 2-[2,6-bis(oxidanyl)phenyl]carbonyl-5-methyl-3-oxidanyl-benzoate


Mass: 302.279 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H14O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
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: 2.76 Å3/Da / Density % sol: 55.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM Tris-HCl (pH8.5), 15% w/v PEG8000, 250 mM KF

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.4→48.73 Å / Num. obs: 17929 / % possible obs: 99.8 % / Redundancy: 19.9 % / Biso Wilson estimate: 50.53 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Net I/σ(I): 25.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 20.5 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 1830 / CC1/2: 0.94 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7F0O

7f0o


Resolution: 2.4→48.73 Å / SU ML: 0.3309 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.2075
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2489 1792 10 %
Rwork0.2075 16122 -
obs0.2117 17914 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.38 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2402 0 44 75 2521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082522
X-RAY DIFFRACTIONf_angle_d1.01783436
X-RAY DIFFRACTIONf_chiral_restr0.0516358
X-RAY DIFFRACTIONf_plane_restr0.0087446
X-RAY DIFFRACTIONf_dihedral_angle_d16.4927338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.470.34451340.25011206X-RAY DIFFRACTION99.63
2.47-2.540.26991350.23971210X-RAY DIFFRACTION99.19
2.54-2.620.35541330.25581203X-RAY DIFFRACTION99.4
2.62-2.710.34231340.27391210X-RAY DIFFRACTION99.63
2.71-2.820.35971350.26371213X-RAY DIFFRACTION99.48
2.82-2.950.32851360.24031216X-RAY DIFFRACTION99.56
2.95-3.110.29761360.23771223X-RAY DIFFRACTION99.78
3.11-3.30.281360.22671224X-RAY DIFFRACTION99.71
3.3-3.560.30261370.22521242X-RAY DIFFRACTION99.78
3.56-3.910.2261390.19641245X-RAY DIFFRACTION99.86
3.91-4.480.23211400.17861261X-RAY DIFFRACTION99.86
4.48-5.640.17821420.1651279X-RAY DIFFRACTION99.93
5.64-48.730.21121550.19941390X-RAY DIFFRACTION99.68

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