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- PDB-7y3w: Crystal structure of an questin oxidase (BTG13) from Cercospora s... -

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Basic information

Entry
Database: PDB / ID: 7y3w
TitleCrystal structure of an questin oxidase (BTG13) from Cercospora sp. JNU001
Componentsquestin oxidase
KeywordsOXIDOREDUCTASE / metalloenzyme / carboxylated-lysine
Function / homology:
Function and homology information
Biological speciesCercospora sojina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsHou, X.D. / Fu, K. / Rao, Y.J.
Funding support China, 4items
OrganizationGrant numberCountry
Other private2018YFA0901700 China
Other privateJUSRP12015 China
Other private2020M671329 China
Other private2020Z383 China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Discovery of the Biosynthetic Pathway of Beticolin 1 Reveals a Novel Non-Heme Iron-Dependent Oxygenase for Anthraquinone Ring Cleavage.
Authors: Hou, X. / Xu, H. / Deng, Z. / Yan, Y. / Yuan, Z. / Liu, X. / Su, Z. / Yang, S. / Zhang, Y. / Rao, Y.
History
DepositionJun 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: questin oxidase
B: questin oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,13815
Polymers100,0142
Non-polymers1,12513
Water14,700816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-43 kcal/mol
Surface area32240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.781, 99.618, 130.638
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein questin oxidase


Mass: 50006.801 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cercospora sojina (fungus) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 816 / 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: 2.59 Å3/Da / Density % sol: 52.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.45 / Details: 0.1 M Bis-Tris pH 6.45, 16% PEG10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 80589 / % possible obs: 98.7 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.051 / Rrim(I) all: 0.154 / Χ2: 0.844 / Net I/σ(I): 4.6 / Num. measured all: 709190
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.9770.79971510.7060.310.8610.91588.9
1.97-2.058.70.60780030.8740.2140.6450.999.1
2.05-2.149.10.47780470.9230.1650.5060.91299.7
2.14-2.258.90.34481070.9550.1210.3650.90599.9
2.25-2.398.80.25980750.9690.0920.2760.91799.7
2.39-2.589.20.20280680.9810.0690.2140.87599.9
2.58-2.848.70.14781720.9870.0520.1560.83399.9
2.84-3.259.40.10381790.9940.0350.1080.816100
3.25-4.099.10.05582520.9970.0190.0580.75899.9
4.09-508.90.03885350.9980.0130.0410.64899.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→42.1 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.571 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1817 3927 4.9 %RANDOM
Rwork0.1499 ---
obs0.1515 75735 97.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.09 Å2 / Biso mean: 20.406 Å2 / Biso min: 11.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0 Å2-0 Å2
2---0.08 Å20 Å2
3---0.31 Å2
Refinement stepCycle: final / Resolution: 1.9→42.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6918 0 68 816 7802
Biso mean--36.04 30.7 -
Num. residues----880
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0137157
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176610
X-RAY DIFFRACTIONr_angle_refined_deg1.6461.649693
X-RAY DIFFRACTIONr_angle_other_deg1.4571.57515274
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9295882
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.45521.34388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.503151088
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3471554
X-RAY DIFFRACTIONr_chiral_restr0.0890.2890
X-RAY DIFFRACTIONr_gen_planes_refined0.010.028064
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021602
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 220 -
Rwork0.213 4268 -
all-4488 -
obs--75.56 %

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