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- PDB-6xlt: The 1.48 Angstrom crystal structure of evolved galactose oxidase ... -

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Basic information

Entry
Database: PDB / ID: 6xlt
TitleThe 1.48 Angstrom crystal structure of evolved galactose oxidase variant A3.E7
ComponentsGalactose oxidase
KeywordsOXIDOREDUCTASE / Cys-Tyr cofactor
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 speciesGibberella zeae (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.478 Å
AuthorsLiu, A. / Li, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM108988 United States
National Science Foundation (NSF, United States)CHE-1808637 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Formation of Monofluorinated Radical Cofactor in Galactose Oxidase through Copper-Mediated C-F Bond Scission.
Authors: Li, J. / Davis, I. / Griffith, W.P. / Liu, A.
History
DepositionJun 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galactose oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1186
Polymers69,8041
Non-polymers3145
Water13,601755
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, MONOMER
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.282, 89.120, 86.162
Angle α, β, γ (deg.)90.000, 117.820, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1752-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Galactose oxidase / / GOase


Mass: 69803.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gibberella zeae (fungus) / Gene: GAOA / Production host: Escherichia coli (E. coli) / References: UniProt: P0CS93, galactose oxidase

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Non-polymers , 5 types, 760 molecules

#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 755 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.287 Å3/Da / Density % sol: 46.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 10% PEG 6000, 0.1 M CaCl2, 5% glycerol, 10 mM N-Acetylglucosamine and 50 mM acetic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 22, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.478→50 Å / Num. obs: 108128 / % possible obs: 99.9 % / Redundancy: 5 % / Biso Wilson estimate: 18.09 Å2 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.03 / Rrim(I) all: 0.068 / Χ2: 1.032 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.48-1.514.20.95971160.6460.5171.0960.74499
1.51-1.554.80.82271690.6580.4150.9250.85499.9
1.55-1.594.90.69271780.7230.3470.7780.80699.9
1.59-1.6450.51972090.8170.260.5830.829100
1.64-1.6950.42772210.8710.2140.4790.862100
1.69-1.7550.33371490.9150.1670.3740.925100
1.75-1.8250.25372260.9490.1270.2840.971100
1.82-1.9150.19171980.9670.0950.2141.071100
1.91-2.0150.1472070.9780.070.1581.234100
2.01-2.1350.10472210.9890.0520.1161.357100
2.13-2.35.10.07971940.9920.040.0891.315100
2.3-2.535.10.0672650.9960.030.0671.178100
2.53-2.95.10.04572290.9980.0220.051.136100
2.9-3.655.10.0372620.9990.0150.0340.978100
3.65-504.90.02972840.9990.0150.0321.12799.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.9refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GOG

1gog


Resolution: 1.478→28.461 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1692 2000 1.85 %
Rwork0.1477 106106 -
obs0.1481 108106 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.58 Å2 / Biso mean: 26.1572 Å2 / Biso min: 11.04 Å2
Refinement stepCycle: final / Resolution: 1.478→28.461 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4832 0 16 755 5603
Biso mean--37.29 38.65 -
Num. residues----639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065113
X-RAY DIFFRACTIONf_angle_d1.0677003
X-RAY DIFFRACTIONf_chiral_restr0.045760
X-RAY DIFFRACTIONf_plane_restr0.006927
X-RAY DIFFRACTIONf_dihedral_angle_d11.9691844
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4781-1.51510.30931380.2718729997
1.5151-1.5560.24931430.24617558100
1.556-1.60180.25031420.22287588100
1.6018-1.65350.24271440.19587600100
1.6535-1.71260.19321420.17667544100
1.7126-1.78120.18361430.16887598100
1.7812-1.86220.18611430.15687572100
1.8622-1.96040.17371420.15127583100
1.9604-2.08320.16841430.14647597100
2.0832-2.24390.17121440.14517591100
2.2439-2.46970.18641430.14777612100
2.4697-2.82670.18541440.14787620100
2.8267-3.56030.13961440.13577654100
3.5603-28.4610.13841450.1194769099
Refinement TLS params.Method: refined / Origin x: -35.7023 Å / Origin y: -8.038 Å / Origin z: 20.4101 Å
111213212223313233
T0.1334 Å20.019 Å2-0.0025 Å2-0.1324 Å20.0021 Å2--0.1345 Å2
L0.4339 °2-0.0669 °2-0.1352 °2-0.5014 °20.1048 °2--0.7534 °2
S0.0104 Å °0.0522 Å °-0.0009 Å °-0.0842 Å °-0.0113 Å °-0.0402 Å °0.0111 Å °0.0462 Å °-0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 1002
2X-RAY DIFFRACTION1allS1 - 2002

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