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- PDB-7y3y: Crystal structure of BTG13 mutant (T299V) -

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Basic information

Entry
Database: PDB / ID: 7y3y
TitleCrystal structure of BTG13 mutant (T299V)
Componentsquestin oxidase BTG13
KeywordsOXIDOREDUCTASE / metalloenzyme / carboxylated-lysine
Function / homology:
Function and homology information
Biological speciesCercospora sojina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 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
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

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Assembly

Deposited unit
A: questin oxidase BTG13
B: questin oxidase BTG13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,0946
Polymers98,7982
Non-polymers2964
Water12,088671
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-44 kcal/mol
Surface area32450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.310, 99.558, 129.781
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 BTG13


Mass: 49399.094 Da / Num. of mol.: 2 / Mutation: T299V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cercospora sojina (fungus) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 671 / 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: 52.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion / 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: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.92→78.99 Å / Num. obs: 77631 / % possible obs: 99 % / Redundancy: 7.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.039 / Rrim(I) all: 0.112 / Net I/σ(I): 14.8 / Num. measured all: 610127 / Scaling rejects: 18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.92-2.047.30.61787732120980.9190.2380.6642.996.9
5.77-78.997.50.0362350431420.9990.0140.03939.899.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7Y3W

7y3w


Resolution: 1.92→78.99 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.456 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2005 3911 5 %RANDOM
Rwork0.1702 ---
obs0.1717 73649 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.11 Å2 / Biso mean: 25.432 Å2 / Biso min: 12.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å2-0 Å2-0 Å2
2---3.18 Å20 Å2
3---3.08 Å2
Refinement stepCycle: final / Resolution: 1.92→78.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6912 0 14 671 7597
Biso mean--32.76 33.04 -
Num. residues----880
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0137098
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176554
X-RAY DIFFRACTIONr_angle_refined_deg1.5751.6339624
X-RAY DIFFRACTIONr_angle_other_deg1.4481.57615142
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1115878
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.22921.518382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.377151156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8941552
X-RAY DIFFRACTIONr_chiral_restr0.0830.2886
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028024
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021588
LS refinement shellResolution: 1.925→1.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 262 -
Rwork0.297 5056 -
all-5318 -
obs--92.66 %

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