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- PDB-2eib: Crystal Structure of Galactose Oxidase, W290H mutant -

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Basic information

Entry
Database: PDB / ID: 2eib
TitleCrystal Structure of Galactose Oxidase, W290H mutant
ComponentsGalactose oxidase
KeywordsOXIDOREDUCTASE / Galactose Oxidase mutant
Function / homology
Function and homology information


galactose oxidase / galactose oxidase activity / extracellular region / metal ion binding
Similarity search - Function
Galactose oxidase/kelch, beta-propeller / 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 motif / Kelch / Kelch repeat type 1 / Coagulation factors 5/8 type C domain (FA58C) profile. ...Galactose oxidase/kelch, beta-propeller / 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 motif / 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 domain-like / 7 Propeller / Methylamine Dehydrogenase; Chain H / Galactose-binding-like domain superfamily / Immunoglobulin E-set / Jelly Rolls / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / COPPER (II) ION / Galactose oxidase / Galactose oxidase
Similarity search - Component
Biological speciesGibberella zeae (fungus)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsPhillips, S.E. / McPherson, M.J. / Knowles, P.F. / Wilmot, C.
Citation
Journal: Biochemistry / Year: 2007
Title: The Stacking Tryptophan of Galactose Oxidase: A Second-Coordination Sphere Residue that Has Profound Effects on Tyrosyl Radical Behavior and Enzyme Catalysis
Authors: Rogers, M.S. / Tyler, E.M. / Akyumani, N. / Kurtis, C.R. / Spooner, R.K. / Deacon, S.E. / Tamber, S. / Firbank, S.J. / Mahmoud, K. / Knowles, P.F. / Phillips, S.E. / McPherson, M.J. / Dooley, D.M.
#1: Journal: J.Biol.Chem. / Year: 1994
Title: Structure and mechanism of galactose oxidase. The free radical site
Authors: Baron, A.J. / Stevens, C. / Wilmot, C. / Seneviratne, K.D. / Blakeley, V. / Dooley, D.M. / Phillips, S.E. / Knowles, P.F. / McPherson, M.J.
History
DepositionMar 12, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)68,8907
Polymers68,5311
Non-polymers3606
Water5,873326
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.000, 89.400, 86.700
Angle α, β, γ (deg.)90.000, 117.800, 90.000
Int Tables number4
Space group name H-MP1211
DetailsProtein is a monomer in the asymmetric unit

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Galactose oxidase / GAO


Mass: 68530.531 Da / Num. of mol.: 1 / Fragment: residues 1-639 / Mutation: W290H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gibberella zeae (fungus) / Gene: go / Plasmid: pGOF1 / Production host: Emericella nidulans (mold) / Strain (production host): G191
References: UniProt: Q01745, UniProt: P0CS93*PLUS, galactose oxidase

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Non-polymers , 5 types, 332 molecules

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


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.9 Å3/Da / Density % sol: 74.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 1-2M Amonium Sulphate, 0.1M sodium acetate pH 4-5, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Rsym value: 0.046

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1GOG

1gog


Resolution: 2.1→10 Å / Rfactor Rwork: 0.157 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Displacement parametersBiso mean: 24.376 Å2
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4826 0 19 326 5171
Refine LS restraintsType: p_bond_d / Dev ideal: 0.017

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