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- PDB-7y3x: Crystal structure of BTG13 mutant (H58F) -

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Basic information

Entry
Database: PDB / ID: 7y3x
TitleCrystal structure of BTG13 mutant (H58F)
ComponentsQuestin oxidase
KeywordsOXIDOREDUCTASE / metalloenzyme / carboxylated-lysine
Function / homology:
Function and homology information
Biological speciesCercospora sojina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsHou, X.D. / 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
B: Questin oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2026
Polymers98,9062
Non-polymers2964
Water7,548419
1
A: Questin oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6013
Polymers49,4531
Non-polymers1482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-15 kcal/mol
Surface area16900 Å2
MethodPISA
2
B: Questin oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6013
Polymers49,4531
Non-polymers1482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-15 kcal/mol
Surface area16980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.292, 99.742, 129.435
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: 49453.094 Da / Num. of mol.: 2 / Mutation: H58F
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


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / 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: 52.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / 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: 2.14→79.01 Å / Num. obs: 57432 / % possible obs: 99.8 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.04 / Rrim(I) all: 0.146 / Net I/σ(I): 16.2 / Num. measured all: 757621 / Scaling rejects: 8
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
2.14-2.2513.31.10111043682790.8980.3091.1452.6100
6.76-79.0111.80.03223484199010.010.03453.699.2

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Processing

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

7y3w


Resolution: 2.14→79.01 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.123 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2096 2799 4.9 %RANDOM
Rwork0.1737 ---
obs0.1755 54567 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.71 Å2 / Biso mean: 34.43 Å2 / Biso min: 17.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å2-0 Å2-0 Å2
2---3.21 Å20 Å2
3---3.11 Å2
Refinement stepCycle: final / Resolution: 2.14→79.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6920 0 14 419 7353
Biso mean--43.72 38.43 -
Num. residues----880
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0137106
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176550
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.6349634
X-RAY DIFFRACTIONr_angle_other_deg1.3791.57515134
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3455878
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.09221.458384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.891151148
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3361552
X-RAY DIFFRACTIONr_chiral_restr0.0790.2888
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028040
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021596
LS refinement shellResolution: 2.14→2.193 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.271 203 -
Rwork0.269 3976 -
obs--99.81 %

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