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- PDB-5niw: Glucose oxydase mutant A2 -

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Basic information

Entry
Database: PDB / ID: 5niw
TitleGlucose oxydase mutant A2
ComponentsGlucose oxidase
KeywordsOXIDOREDUCTASE / oxygen activation / His516 conformation
Function / homology
Function and homology information


glucose oxidase / glucose oxidase activity / flavin adenine dinucleotide binding / extracellular region
Similarity search - Function
Glucose Oxidase; domain 2 / Glucose Oxidase, domain 2 / Glucose Oxidase; domain 3 / Glucose Oxidase, domain 3 / Glucose Oxidase, domain 2 / GMC oxidoreductases signature 1. / GMC oxidoreductases signature 2. / Glucose-methanol-choline oxidoreductase / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase ...Glucose Oxidase; domain 2 / Glucose Oxidase, domain 2 / Glucose Oxidase; domain 3 / Glucose Oxidase, domain 3 / Glucose Oxidase, domain 2 / GMC oxidoreductases signature 1. / GMC oxidoreductases signature 2. / Glucose-methanol-choline oxidoreductase / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Few Secondary Structures / Irregular / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / FLAVIN-ADENINE DINUCLEOTIDE / OXYGEN MOLECULE / O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL / DI(HYDROXYETHYL)ETHER / Glucose oxidase
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsHoffmann, K. / Frank, D.
CitationJournal: ACS Catal / Year: 2017
Title: Shuffling Active Site Substate Populations Affects Catalytic Activity: The Case of Glucose Oxidase.
Authors: Petrovic, D. / Frank, D. / Kamerlin, S.C.L. / Hoffmann, K. / Strodel, B.
History
DepositionMar 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2018Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucose oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,52425
Polymers63,0961
Non-polymers4,42824
Water6,557364
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6890 Å2
ΔGint68 kcal/mol
Surface area21130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.100, 128.100, 77.650
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Glucose oxidase / Beta-D-glucose:oxygen 1-oxido-reductase / Glucose oxyhydrase / GOD


Mass: 63095.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus niger (mold) / Gene: gox / Production host: Komagataella pastoris (fungus) / References: UniProt: P13006, glucose oxidase

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Sugars , 2 types, 6 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 382 molecules

#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#6: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C4H8O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-P4C / O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL / POLYETHYLENE 400


Mass: 324.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O8
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H2O

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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: 2.91 Å3/Da / Density % sol: 57.8 %
Crystal growTemperature: 280 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100 mM HEPES 45% v/v dioxane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.79→41.93 Å / Num. obs: 67817 / % possible obs: 98.3 % / Redundancy: 11.1 % / Net I/σ(I): 12.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementResolution: 1.8→110.94 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.601 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19089 3389 5 %RANDOM
Rwork0.15401 ---
obs0.15583 64400 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 0.5 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.959 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.12 Å20 Å2
2--0.23 Å2-0 Å2
3----0.76 Å2
Refinement stepCycle: 1 / Resolution: 1.8→110.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4401 0 294 364 5059
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0194838
X-RAY DIFFRACTIONr_bond_other_d0.0020.024264
X-RAY DIFFRACTIONr_angle_refined_deg2.2061.9956580
X-RAY DIFFRACTIONr_angle_other_deg1.17739924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4575583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25724.554213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.15815664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0471521
X-RAY DIFFRACTIONr_chiral_restr0.1330.2727
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0215317
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02953
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_it1.2811.8492318
X-RAY DIFFRACTIONr_mcbond_other1.2631.8472317
X-RAY DIFFRACTIONr_mcangle_it1.7472.7642896
X-RAY DIFFRACTIONr_mcangle_other1.752.7662897
X-RAY DIFFRACTIONr_scbond_it2.2492.2352520
X-RAY DIFFRACTIONr_scbond_other2.2422.2352520
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.33.2233682
X-RAY DIFFRACTIONr_long_range_B_refined4.68423.9615633
X-RAY DIFFRACTIONr_long_range_B_other4.68723.9695634
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.802→1.849 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 236 -
Rwork0.234 4608 -
obs--97.45 %
Refinement TLS params.Method: refined / Origin x: 21.6328 Å / Origin y: 162.6945 Å / Origin z: 80.7387 Å
111213212223313233
T0.0176 Å2-0.0198 Å2-0.0007 Å2-0.0299 Å20.0043 Å2--0.0068 Å2
L0.4317 °20.2448 °2-0.0969 °2-0.4483 °2-0.1124 °2--0.2272 °2
S0.0454 Å °-0.0457 Å °-0.0016 Å °0.053 Å °-0.0167 Å °0.0292 Å °-0.0162 Å °0.023 Å °-0.0287 Å °

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