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- PDB-8tx6: Crystal structure of an engineered variant of galactose oxidase, ... -

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Basic information

Entry
Database: PDB / ID: 8tx6
TitleCrystal structure of an engineered variant of galactose oxidase, GOaseRd7BB, from Fusarium graminearum
ComponentsGalactose oxidase
KeywordsOXIDOREDUCTASE / galactose oxidase / Islatravir / Aerobic Oxidation / Biocatalytic oxidation / (R)-ethynyl-glyceraldehyde 3-phosphate
Function / homology
Function and homology information


galactose oxidase / galactose oxidase activity / extracellular region / metal ion binding
Similarity search - Function
Galactose oxidase-like, Early set domain / Galactose oxidase, central domain superfamily / Galactose oxidase-like, Early set domain / Galactose oxidase/kelch, beta-propeller / Coagulation factor 5/8 C-terminal domain, discoidin domain / Kelch / Kelch repeat type 1 / Kelch motif / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain ...Galactose oxidase-like, Early set domain / Galactose oxidase, central domain superfamily / Galactose oxidase-like, Early set domain / Galactose oxidase/kelch, beta-propeller / Coagulation factor 5/8 C-terminal domain, discoidin domain / Kelch / Kelch repeat type 1 / Kelch motif / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding-like domain superfamily / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
ACETATE ION / COPPER (II) ION / Galactose oxidase
Similarity search - Component
Biological speciesFusarium graminearum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsSelvaraj, B. / Orth, P.
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: Chemrxiv / Year: 2023
Title: Development of a Biocatalytic Aerobic Oxidation for the Manufacturing Route to Islatravir
Authors: Shaw, M.H. / Fryszkowska, A. / Alvizo, O. / Attadgie, I. / Borra-Garske, M. / Devine, P.N. / Duan, D. / Grosser, S.T. / Forstater, J.H. / Hughes, G.J. / Maloney, K.M. / Margelefsky, E. / ...Authors: Shaw, M.H. / Fryszkowska, A. / Alvizo, O. / Attadgie, I. / Borra-Garske, M. / Devine, P.N. / Duan, D. / Grosser, S.T. / Forstater, J.H. / Hughes, G.J. / Maloney, K.M. / Margelefsky, E. / Mattern, K.A. / Miller, M.T. / Nawrat, C.C. / Nazor, J. / Orth, P. / Ouimet, C.M. / Robaire, S.A. / Ruccolo, S. / Schwalm, E.L. / Verma, D. / Xiao, L. / Selvaraj, B. / Zhang, V.
History
DepositionAug 22, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Galactose oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1764
Polymers70,0131
Non-polymers1633
Water7,638424
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.623, 88.920, 86.167
Angle α, β, γ (deg.)90.000, 117.820, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-803-

HOH

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Components

#1: Protein Galactose oxidase


Mass: 70013.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium graminearum (fungus) / Gene: GAOA / Production host: Escherichia coli (E. coli) / References: UniProt: P0CS93
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.36 Å3/Da / Density % sol: 47.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 20% vol PEG 3350, 4% vol Tacsimate, 100 mM acetate buffer (pH 4.6)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.56→22.75 Å / Num. obs: 79190 / % possible obs: 85.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 22.62 Å2 / CC1/2: 0.999 / Net I/σ(I): 15
Reflection shellResolution: 1.76→1.85 Å / Num. unique obs: 79190 / CC1/2: 0.857

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MOSFLMdata reduction
Aimlessdata scaling
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→22.75 Å / SU ML: 0.1712 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.172
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.188 3891 4.91 %
Rwork0.1642 75292 -
obs0.1654 79183 85.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.91 Å2
Refinement stepCycle: LAST / Resolution: 1.56→22.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4817 0 6 424 5247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01164952
X-RAY DIFFRACTIONf_angle_d1.15826764
X-RAY DIFFRACTIONf_chiral_restr0.0821737
X-RAY DIFFRACTIONf_plane_restr0.0095890
X-RAY DIFFRACTIONf_dihedral_angle_d5.9009687
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.580.380340.286783X-RAY DIFFRACTION2.64
1.58-1.60.2253150.2605276X-RAY DIFFRACTION8.92
1.6-1.620.3382520.2624842X-RAY DIFFRACTION26.94
1.62-1.640.2571640.24971361X-RAY DIFFRACTION43.3
1.64-1.660.2884810.24971758X-RAY DIFFRACTION55.91
1.66-1.690.26281170.2412271X-RAY DIFFRACTION71.39
1.69-1.710.26521260.23592720X-RAY DIFFRACTION87.35
1.71-1.740.26121550.23843088X-RAY DIFFRACTION97.01
1.74-1.770.29091770.24863109X-RAY DIFFRACTION99.79
1.77-1.80.27571480.24163134X-RAY DIFFRACTION99.91
1.8-1.840.24151660.21973146X-RAY DIFFRACTION99.76
1.84-1.880.21711570.20713154X-RAY DIFFRACTION99.82
1.88-1.920.27351700.19583115X-RAY DIFFRACTION99.85
1.92-1.960.21241490.18613152X-RAY DIFFRACTION99.85
1.96-2.010.23451740.18123139X-RAY DIFFRACTION99.91
2.01-2.070.21271780.18343142X-RAY DIFFRACTION99.88
2.07-2.130.19961570.17853154X-RAY DIFFRACTION99.85
2.13-2.20.19771670.17293106X-RAY DIFFRACTION99.79
2.2-2.270.22021660.16783167X-RAY DIFFRACTION99.88
2.27-2.360.19021620.16563126X-RAY DIFFRACTION99.88
2.36-2.470.19241720.16843138X-RAY DIFFRACTION99.73
2.47-2.60.17661610.16933151X-RAY DIFFRACTION99.82
2.6-2.770.18811570.16733146X-RAY DIFFRACTION99.52
2.77-2.980.19931700.16423138X-RAY DIFFRACTION99.61
2.98-3.280.19761460.16293175X-RAY DIFFRACTION99.43
3.28-3.750.16721580.15313148X-RAY DIFFRACTION99.25
3.75-4.720.13531770.12333141X-RAY DIFFRACTION99.34
4.72-22.750.14131650.12623212X-RAY DIFFRACTION99.18

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