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- PDB-5nit: Glucose oxidase mutant A2 -

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Basic information

Entry
Database: PDB / ID: 5nit
TitleGlucose oxidase 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 / Glucose oxidase
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsHoffmann, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
Germany
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 / diffrn_radiation_wavelength / 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 / pdbx_struct_special_symmetry / 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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _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
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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)67,13626
Polymers63,0821
Non-polymers4,05425
Water7,692427
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint81 kcal/mol
Surface area21100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.657, 128.657, 77.693
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-1004-

HOH

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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: 63081.777 Da / Num. of mol.: 1 / Mutation: T30V I94V A162T R537K M556V
Source method: isolated from a genetically manipulated source
Details: mutant A2 / 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, 4 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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 , 5 types, 448 molecules

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


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


Mass: 88.105 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Formula: C4H8O2
#7: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.94 Å3/Da / Density % sol: 58.2 %
Crystal growTemperature: 280 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 100 mM HEPES 40% v/v dioxane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.86→45.27 Å / Num. obs: 61296 / % possible obs: 98.1 % / Redundancy: 8.2 % / Net I/σ(I): 12.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLM7.2.1data reduction
SCALA6.5.019data scaling
PHASER7.0.20phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CF3

1cf3


Resolution: 1.87→111.42 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.997 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20393 3243 5.3 %RANDOM
Rwork0.16472 ---
obs0.16678 58032 99.45 %-
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: 20.215 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å2-0 Å2
2---0.04 Å20 Å2
3---0.13 Å2
Refinement stepCycle: 1 / Resolution: 1.87→111.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4430 0 270 427 5127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194873
X-RAY DIFFRACTIONr_bond_other_d0.0020.024304
X-RAY DIFFRACTIONr_angle_refined_deg1.9521.9936645
X-RAY DIFFRACTIONr_angle_other_deg1.115310037
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7425599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69824.554213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.9115685
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8591521
X-RAY DIFFRACTIONr_chiral_restr0.1170.2738
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215361
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02959
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_it1.0481.5582343
X-RAY DIFFRACTIONr_mcbond_other1.0411.5562342
X-RAY DIFFRACTIONr_mcangle_it1.6642.3312932
X-RAY DIFFRACTIONr_mcangle_other1.6642.3342933
X-RAY DIFFRACTIONr_scbond_it1.6471.8452528
X-RAY DIFFRACTIONr_scbond_other1.6451.8442528
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5622.6693702
X-RAY DIFFRACTIONr_long_range_B_refined4.25919.8035755
X-RAY DIFFRACTIONr_long_range_B_other4.25919.8085756
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.868→1.916 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 191 -
Rwork0.254 4124 -
obs--95.85 %
Refinement TLS params.Method: refined / Origin x: 87.7078 Å / Origin y: 48.8579 Å / Origin z: 9.6658 Å
111213212223313233
T0.0101 Å2-0.0167 Å2-0.0008 Å2-0.0364 Å20.0013 Å2--0.0031 Å2
L0.3679 °20.0542 °20.044 °2-0.1125 °20.0185 °2--0.1685 °2
S-0.0057 Å °0.0561 Å °-0.014 Å °-0.005 Å °0.0164 Å °0.0108 Å °-0.0181 Å °0.0154 Å °-0.0107 Å °

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