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- PDB-7f13: Crystal structure of isomerase Dcr3 -

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Basic information

Entry
Database: PDB / ID: 7f13
TitleCrystal structure of isomerase Dcr3
ComponentsDcr3
KeywordsISOMERASE / tetrahydroxanthones / blennolides
Biological speciesDiaporthe longicolla (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 1.1Oct 5, 2022Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Nov 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

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Assembly

Deposited unit
A: Dcr3
B: Dcr3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4783
Polymers39,2402
Non-polymers2381
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-8 kcal/mol
Surface area14510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.999, 104.999, 139.958
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-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.84 Å3/Da / Density % sol: 56.66 %
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: 1.08 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.15→49.16 Å / Num. obs: 25477 / % possible obs: 100 % / Redundancy: 21.9 % / Biso Wilson estimate: 42.58 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 39
Reflection shellResolution: 2.15→2.22 Å / Redundancy: 22.9 % / Rmerge(I) obs: 0.697 / Mean I/σ(I) obs: 5.2 / Num. unique obs: 2161 / % possible all: 100

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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: 2.15→49.16 Å / SU ML: 0.2804 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.1758
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2736 1998 7.86 %
Rwork0.2299 23425 -
obs0.2333 25423 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.58 Å2
Refinement stepCycle: LAST / Resolution: 2.15→49.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2428 0 15 137 2580
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00742518
X-RAY DIFFRACTIONf_angle_d0.94683428
X-RAY DIFFRACTIONf_chiral_restr0.0521364
X-RAY DIFFRACTIONf_plane_restr0.0069442
X-RAY DIFFRACTIONf_dihedral_angle_d15.8011891
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20.36911380.30941617X-RAY DIFFRACTION99.83
2.2-2.260.33291390.27711626X-RAY DIFFRACTION99.72
2.26-2.330.35151400.26871650X-RAY DIFFRACTION99.89
2.33-2.410.31891400.25691637X-RAY DIFFRACTION99.89
2.41-2.490.35011420.25091655X-RAY DIFFRACTION100
2.49-2.590.29771370.26391624X-RAY DIFFRACTION99.83
2.59-2.710.32491420.28591650X-RAY DIFFRACTION99.94
2.71-2.850.35151430.29131666X-RAY DIFFRACTION99.94
2.85-3.030.33141410.27311662X-RAY DIFFRACTION99.89
3.03-3.260.32391420.2441663X-RAY DIFFRACTION99.94
3.26-3.590.27261420.23761683X-RAY DIFFRACTION99.89
3.59-4.110.23891460.20081698X-RAY DIFFRACTION100
4.11-5.180.20451480.17521731X-RAY DIFFRACTION100
5.18-49.160.2451580.21971863X-RAY DIFFRACTION100

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