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- PDB-8jpz: The thermostability mutant Gox_M8 from Aspergillus niger -

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Basic information

Entry
Database: PDB / ID: 8jpz
TitleThe thermostability mutant Gox_M8 from Aspergillus niger
ComponentsGlucose oxidase (Fragment)
KeywordsOXIDOREDUCTASE / Glucose oxidase
Function / homology
Function and homology information


beta-D-glucose oxidase activity / glucose oxidase / flavin adenine dinucleotide binding
Similarity search - Function
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 superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / OXYGEN MOLECULE / Glucose oxidase
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsTu, T. / Yan, Y.R.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32072769 China
National Natural Science Foundation of China (NSFC)32222082 China
CitationJournal: Fundam Res / Year: 2024
Title: Revealing the intricate mechanism governing the pH-dependent activity of a quintessential representative of flavoproteins, glucose oxidase
Authors: Tu, T. / Zhang, Y. / Yan, Y. / Li, L. / Liu, X. / Hakulinen, N. / Zhang, W. / Mu, Y. / Luo, H. / Yao, B. / Li, W. / Huang, H.
History
DepositionJun 13, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Jan 1, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucose oxidase (Fragment)
B: Glucose oxidase (Fragment)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,11822
Polymers126,3092
Non-polymers6,80920
Water15,529862
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.450, 126.450, 193.360
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glucose oxidase (Fragment)


Mass: 63154.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus niger (mold) / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: Q5Q041

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Sugars , 2 types, 13 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 2 / Source method: isolated from a natural source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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, 869 molecules

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


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 862 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.07 Å3/Da / Density % sol: 59.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M sodium chloride, 0.1 M HEPES buffer (pH 7.0), and 12% (w/v) polyethylene glycol monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.08→21.18 Å / Num. obs: 94279 / % possible obs: 99.82 % / Redundancy: 2 % / Biso Wilson estimate: 36.31 Å2 / CC1/2: 0.997 / Net I/σ(I): 8.86
Reflection shellResolution: 2.08→2.154 Å / Mean I/σ(I) obs: 1.21 / Num. unique obs: 9278 / CC1/2: 0.54

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→21.18 Å / SU ML: 0.2478 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.6575 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2036 4707 4.99 %
Rwork0.1655 89534 -
obs0.1674 94241 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.79 Å2
Refinement stepCycle: LAST / Resolution: 2.08→21.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8902 0 446 862 10210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00839695
X-RAY DIFFRACTIONf_angle_d0.947113284
X-RAY DIFFRACTIONf_chiral_restr0.05551518
X-RAY DIFFRACTIONf_plane_restr0.00551692
X-RAY DIFFRACTIONf_dihedral_angle_d5.53387519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.10.36691520.29762944X-RAY DIFFRACTION100
2.1-2.130.29111670.26272932X-RAY DIFFRACTION100
2.13-2.150.29671710.24682912X-RAY DIFFRACTION100
2.15-2.180.29341480.24122981X-RAY DIFFRACTION100
2.18-2.210.25151660.23282923X-RAY DIFFRACTION100
2.21-2.240.27531470.23382943X-RAY DIFFRACTION100
2.24-2.270.30041550.22652939X-RAY DIFFRACTION100
2.27-2.310.27041670.22732930X-RAY DIFFRACTION100
2.31-2.340.26271310.20892991X-RAY DIFFRACTION100
2.34-2.380.27661460.19492977X-RAY DIFFRACTION100
2.38-2.420.2411440.1852944X-RAY DIFFRACTION100
2.42-2.470.26921550.18932954X-RAY DIFFRACTION100
2.47-2.510.21551590.18122961X-RAY DIFFRACTION100
2.51-2.560.25061400.17512971X-RAY DIFFRACTION100
2.56-2.620.21431740.17182959X-RAY DIFFRACTION100
2.62-2.680.23861560.18552963X-RAY DIFFRACTION100
2.68-2.750.2481550.18212979X-RAY DIFFRACTION100
2.75-2.820.26021720.17522950X-RAY DIFFRACTION100
2.82-2.90.22571650.17612963X-RAY DIFFRACTION100
2.9-30.23561340.17133007X-RAY DIFFRACTION100
3-3.10.18921520.16882992X-RAY DIFFRACTION99.97
3.1-3.230.22271530.1742993X-RAY DIFFRACTION100
3.23-3.380.22261510.17483002X-RAY DIFFRACTION100
3.38-3.550.19221540.16382992X-RAY DIFFRACTION100
3.55-3.770.16531550.14863026X-RAY DIFFRACTION100
3.77-4.060.17491590.13233031X-RAY DIFFRACTION100
4.06-4.470.15071730.12283011X-RAY DIFFRACTION100
4.47-5.110.13971650.12033064X-RAY DIFFRACTION100
5.11-6.410.1861570.1463103X-RAY DIFFRACTION100
6.41-21.180.16211840.15143197X-RAY DIFFRACTION98.69

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