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- PDB-2wq8: Glycan labelling using engineered variants of galactose oxidase o... -

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Basic information

Entry
Database: PDB / ID: 2wq8
TitleGlycan labelling using engineered variants of galactose oxidase obtained by directed evolution
ComponentsGALACTOSE OXIDASE
KeywordsOXIDOREDUCTASE / KELCH REPEAT / METAL-BINDING / GLYCOENGINEERING / DIRECTED EVOLUTION
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 repeat type 1 / Kelch motif / 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 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 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
ACETIC ACID / COPPER (II) ION / Galactose oxidase / Galactose oxidase
Similarity search - Component
Biological speciesGIBBERELLA ZEAE (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsRannes, J.G. / Ioannou, A. / Willies, S.C. / Behrens, C. / Grogan, G.J. / Flitsch, S.L. / Turner, N.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: Glycoprotein Labeling Using Engineered Variants of Galactose Oxidase Obtained by Directed Evolution.
Authors: Rannes, J.B. / Ioannou, A. / Willies, S.C. / Grogan, G. / Behrens, C. / Flitsch, S.L. / Turner, N.J.
History
DepositionAug 14, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_conn_angle ...pdbx_database_status / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._pdbx_database_status.status_code_sf / _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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)72,24717
Polymers71,1881
Non-polymers1,05916
Water6,882382
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.464, 88.464, 410.846
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 1 molecules A

#1: Protein GALACTOSE OXIDASE / GAO / GOASE / GO


Mass: 71188.477 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: THIO-ETHER BOND BETWEEN CYS228 SG AND TYR272 CE1 / Source: (gene. exp.) GIBBERELLA ZEAE (fungus) / Plasmid: PET16B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q01745, UniProt: P0CS93*PLUS, galactose oxidase

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Non-polymers , 6 types, 398 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 51 TO PRO ENGINEERED RESIDUE IN CHAIN A, MET 111 TO VAL ...ENGINEERED RESIDUE IN CHAIN A, SER 51 TO PRO ENGINEERED RESIDUE IN CHAIN A, MET 111 TO VAL ENGINEERED RESIDUE IN CHAIN A, GLY 236 TO GLU ENGINEERED RESIDUE IN CHAIN A, TRP 331 TO PHE ENGINEERED RESIDUE IN CHAIN A, ARG 371 TO LYS ENGINEERED RESIDUE IN CHAIN A, GLN 447 TO THR ENGINEERED RESIDUE IN CHAIN A, PRO 504 TO ILE ENGINEERED RESIDUE IN CHAIN A, VAL 535 TO ALA ENGINEERED RESIDUE IN CHAIN A, ASN 576 TO ASP

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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: 3.14 Å3/Da / Density % sol: 60.52 % / Description: NONE
Crystal growpH: 5
Details: 10% PEG6K, 0.1 M CACL2, 5% GLYCEROL, 10 MM GLCNAC, 50 M ACETATE PH 5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.19→46.6 Å / Num. obs: 43048 / % possible obs: 91.9 % / Observed criterion σ(I): 0 / Redundancy: 15.1 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 25.34
Reflection shellResolution: 2.19→2.23 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.43 / % possible all: 13.4

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALAdata scaling
MOLREPphasing
REFMACphasing
REFMAC5.5.0066refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1GOF AND 2EID

1gof

2eid


Resolution: 2.19→76.7 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.887 / SU B: 4.058 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.221 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.24175 2174 5.1 %RANDOM
Rwork0.18212 ---
obs0.18515 40873 85.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.489 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20.31 Å20 Å2
2--0.62 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 2.19→76.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4826 0 64 382 5272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0225011
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1131.9376814
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4025640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44224.028211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.03315729
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.291526
X-RAY DIFFRACTIONr_chiral_restr0.1480.2737
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213875
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_it1.0651.53175
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.78725127
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.30231836
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.7854.51686
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.19→2.247 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 35 -
Rwork0.302 685 -
obs--19.98 %

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