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- PDB-9g43: Crystal structure of a galactose oxidase from Pseudoarthrobacter ... -

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Basic information

Entry
Database: PDB / ID: 9g43
TitleCrystal structure of a galactose oxidase from Pseudoarthrobacter siccitolerans
Components
  • Galactose oxidase
  • SER-HIS-SER-SER-GLY-ALA-ALA
KeywordsOXIDOREDUCTASE / galactose oxidase / Auxiliary Activity 5 family / biocatalysis.
Function / homology
Function and homology information


galactose oxidase / galactose oxidase activity / carbohydrate metabolic process
Similarity search - Function
Calicin, beta-propeller domain / Galactose oxidase-like, Early set domain / Galactose oxidase, central domain superfamily / Galactose oxidase-like, Early set domain / Galactose oxidase/kelch, beta-propeller / Kelch / Kelch repeat type 1 / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain ...Calicin, beta-propeller domain / Galactose oxidase-like, Early set domain / Galactose oxidase, central domain superfamily / Galactose oxidase-like, Early set domain / Galactose oxidase/kelch, beta-propeller / Kelch / Kelch repeat type 1 / 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
BROMIDE ION / Galactose oxidase
Similarity search - Component
Biological speciesPseudarthrobacter siccitolerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsBorges, P.T. / Frazao, T. / Frazao, C. / Martins, L.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Foundation for Science and Technology (FCT) Portugal
CitationJournal: To Be Published
Title: Unraveling the Catalytic and Structural Properties of a New Bacterial Galactose Oxidase
Authors: Taborda, A. / Frazao, T. / Borges, P.T. / Martins, L.
History
DepositionJul 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galactose oxidase
Q: SER-HIS-SER-SER-GLY-ALA-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,49911
Polymers64,6882
Non-polymers8109
Water13,529751
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-7 kcal/mol
Surface area22160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.271, 62.943, 183.284
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AQ

#1: Protein Galactose oxidase


Mass: 64071.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudarthrobacter siccitolerans (bacteria)
Gene: GAOA, ARTSIC4J27_1011 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A024GZ97, galactose oxidase
#2: Protein/peptide SER-HIS-SER-SER-GLY-ALA-ALA


Mass: 616.603 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudarthrobacter siccitolerans (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 6 types, 760 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 751 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium HEPES and MOPS pH 7.5, 0.03 M magnesium chloride hexahydrate, 0.03 M calcium chloride dihydrate, 12.5% (v/v) MPD, 12.5% (w/v) PEG 1000 and 12.5% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.2→91.64 Å / Num. obs: 138716 / % possible obs: 92.6 % / Redundancy: 4.2 % / CC1/2: 0.997 / Net I/σ(I): 8.2
Reflection shellResolution: 1.2→1.29 Å / Num. unique obs: 6936 / CC1/2: 0.613

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata scaling
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→91.64 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.808 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.16609 6747 4.9 %RANDOM
Rwork0.13373 ---
obs0.13532 131969 79.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.781 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å2-0 Å2-0 Å2
2---2.02 Å20 Å2
3---1.21 Å2
Refinement stepCycle: 1 / Resolution: 1.2→91.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4547 0 46 751 5344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0114853
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.6496665
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1265664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.017531
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.89810669
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1150.2756
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023852
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8651.1392587
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.7352.0553259
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.5391.3332266
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined14.42718.017713
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr4.47234853
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.203→1.235 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 18 -
Rwork0.245 509 -
obs--4.16 %

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