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- PDB-2eic: Crystal Structure of Galactose Oxidase mutant W290F -

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Basic information

Entry
Database: PDB / ID: 2eic
TitleCrystal Structure of Galactose Oxidase mutant W290F
ComponentsGalactose oxidase
KeywordsOXIDOREDUCTASE / Galactose Oxidase W290F 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 / Kelch motif / 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 / Kelch motif / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (I) ION / Galactose oxidase / Galactose oxidase
Similarity search - Component
Biological speciesGibberella zeae (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.8 Å
AuthorsAkyumani, N. / Tamber, S. / Firbank, S.J. / Knowles, P.F. / Phillips, S.E. / McPherson, M.J.
CitationJournal: 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.
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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 1.5Oct 30, 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)68,6263
Polymers68,5401
Non-polymers872
Water3,963220
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.77, 88.89, 86.19
Angle α, β, γ (deg.)90.000, 117.9, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Galactose oxidase / GAO


Mass: 68539.555 Da / Num. of mol.: 1 / Fragment: residues 1-639 / Mutation: W290F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gibberella zeae (fungus) / Gene: GO / Production host: Pichia pastoris (fungus)
References: UniProt: Q01745, UniProt: P0CS93*PLUS, galactose oxidase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O
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: 2.41 Å3/Da / Density % sol: 49.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 1-2M Ammonium Sulphate, 0.1M sodium acetate pH 4-5, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.864 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.864 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 14432 / % possible obs: 89.3 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.084

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1GOG

1gog


Resolution: 2.8→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1445 8.9 %random
Rwork0.177 ---
obs-14432 89.3 %-
Solvent computationBsol: 21.815 Å2
Displacement parametersBiso mean: 25.13 Å2
Baniso -1Baniso -2Baniso -3
1--2.444 Å20 Å2-1.801 Å2
2--0.845 Å20 Å2
3---1.599 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4826 0 2 220 5048
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it3.022.5
X-RAY DIFFRACTIONc_scbond_it5.4974
X-RAY DIFFRACTIONc_mcangle_it4.7554
X-RAY DIFFRACTIONc_scangle_it7.2895.5
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.55
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_cysy.param
X-RAY DIFFRACTION2CNS_TOPPAR:water.param
X-RAY DIFFRACTION3ion.param

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