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- PDB-9h7z: Aspergillus niger Glucose Oxidase bound to Ba2+ ions -

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Basic information

Entry
Database: PDB / ID: 9h7z
TitleAspergillus niger Glucose Oxidase bound to Ba2+ ions
ComponentsGlucose oxidase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


beta-D-glucose oxidase activity / glucose oxidase / secondary metabolite biosynthetic process / flavin adenine dinucleotide binding / extracellular region / cytoplasm
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
: / BROMIDE ION / FLAVIN-ADENINE DINUCLEOTIDE / alpha-D-mannopyranose / Glucose oxidase
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsBauer, J.A. / Bauerova, V.
Funding support Slovakia, 1items
OrganizationGrant numberCountry
Other governmentVEGA-2/0081/24 Slovakia
CitationJournal: To Be Published
Title: Aspergillus niger Glucose Oxidase bound to Ba2+ ions
Authors: Bauer, J.A. / Bauerova, V.
History
DepositionOct 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucose oxidase
M: Glucose oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,15152
Polymers131,3922
Non-polymers9,76050
Water11,962664
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.219, 82.251, 103.300
Angle α, β, γ (deg.)90.000, 106.267, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 3 through 56 or resid 58...
d_2ens_1(chain "M" and (resid 3 through 56 or resid 58...
d_1ens_2chain "J"
d_2ens_2chain "V"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1GLYGLYSERSERAA3 - 5625 - 78
d_12ens_1ARGARGTYRTYRAA58 - 8080 - 102
d_13ens_1THRTHRASPASPAA82 - 134104 - 156
d_14ens_1VALVALVALVALAA136 - 186158 - 208
d_15ens_1ALAALATHRTHRAA188 - 276210 - 298
d_16ens_1ASNASNSERSERAA278 - 336300 - 358
d_17ens_1ILEILEGLUGLUAA338 - 374360 - 396
d_18ens_1TRPTRPTYRTYRAA376 - 399398 - 421
d_19ens_1ASPASPARGARGAA401 - 472423 - 494
d_110ens_1ILEILEMETMETAA474 - 523496 - 545
d_111ens_1PROPROSERSERAA525 - 557547 - 579
d_112ens_1HISHISGLNGLNAA559 - 583581 - 605
d_21ens_1GLYGLYSERSERMB3 - 5625 - 78
d_22ens_1ARGARGTYRTYRMB58 - 8080 - 102
d_23ens_1THRTHRASPASPMB82 - 134104 - 156
d_24ens_1VALVALVALVALMB136 - 186158 - 208
d_25ens_1ALAALATHRTHRMB188 - 276210 - 298
d_26ens_1ASNASNSERSERMB278 - 336300 - 358
d_27ens_1ILEILEGLUGLUMB338 - 374360 - 396
d_28ens_1TRPTRPTYRTYRMB376 - 399398 - 421
d_29ens_1ASPASPARGARGMB401 - 472423 - 494
d_210ens_1ILEILEMETMETMB474 - 523496 - 545
d_211ens_1PROPROSERSERMB525 - 557547 - 579
d_212ens_1HISHISGLNGLNMB559 - 583581 - 605
d_11ens_2FADFADFADFADAO606
d_21ens_2FADFADFADFADMNA606

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.87864041219, 0.207043314127, 0.430260493355), (0.209840963855, -0.976852405114, 0.0415469434624), (0.428903014626, 0.0537814531054, -0.901748168474)-9.05953095855, -25.3267937866, 51.3918476696
2given(0.878419563952, 0.202299394349, 0.432959610948), (0.207817057942, -0.97753711403, 0.0351178177317), (0.430338401836, 0.0591282144163, -0.90072899041)-9.18197409476, -24.9811411646, 51.3408214649

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Components

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Protein , 1 types, 2 molecules AM

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


Mass: 65695.883 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Aspergillus niger (mold) / References: UniProt: P13006, glucose oxidase

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Sugars , 5 types, 11 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-6]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-f1_d2-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-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: 1397.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpb1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-2-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-h1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: 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.: 3 / Source method: obtained synthetically / 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 , 7 types, 703 molecules

#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#9: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#10: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#11: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ba
#12: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 664 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.65 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 20% PEG 4000, 0.2 M sodium bromide, 2 mM barium chloride, 30 mM sodium acetate
PH range: 4.5-4.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97624 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Nov 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 1.7→99.16 Å / Num. obs: 147832 / % possible obs: 99.1 % / Redundancy: 7 % / Biso Wilson estimate: 30.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.051 / Net I/σ(I): 10.9
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 7.2 % / Rmerge(I) obs: 2.687 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 7341 / CC1/2: 0.294 / Rpim(I) all: 1.647 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5127refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→37.95 Å / SU ML: 0.2599 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.2175
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1989 7394 5.05 %
Rwork0.1766 138896 -
obs0.1777 146290 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.95 Å2
Refinement stepCycle: LAST / Resolution: 1.71→37.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8912 0 521 664 10097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00759679
X-RAY DIFFRACTIONf_angle_d0.89713224
X-RAY DIFFRACTIONf_chiral_restr0.05271532
X-RAY DIFFRACTIONf_plane_restr0.011682
X-RAY DIFFRACTIONf_dihedral_angle_d14.8633256
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.417917844154
ens_2d_2OAX-RAY DIFFRACTIONTorsion NCS0.07147638402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.730.49592530.40424578X-RAY DIFFRACTION99.51
1.73-1.750.39942380.39554696X-RAY DIFFRACTION99.48
1.75-1.770.36072610.35084591X-RAY DIFFRACTION99.63
1.77-1.790.32612540.334612X-RAY DIFFRACTION99.37
1.79-1.820.34332420.30274666X-RAY DIFFRACTION99.45
1.82-1.840.30762310.28764628X-RAY DIFFRACTION99.69
1.84-1.870.26962580.27124658X-RAY DIFFRACTION99.53
1.87-1.90.29082630.25254608X-RAY DIFFRACTION99.45
1.9-1.930.27332530.2594586X-RAY DIFFRACTION99.08
1.93-1.960.28952310.23524605X-RAY DIFFRACTION98.29
1.96-1.990.26752260.22174561X-RAY DIFFRACTION97.48
1.99-2.030.23912150.21754426X-RAY DIFFRACTION94.12
2.03-2.070.2192590.20854543X-RAY DIFFRACTION97.7
2.07-2.110.22782370.19764682X-RAY DIFFRACTION99.94
2.11-2.150.21182340.18534687X-RAY DIFFRACTION99.94
2.15-2.20.19812540.17524624X-RAY DIFFRACTION99.73
2.2-2.260.20492450.18544621X-RAY DIFFRACTION99.47
2.26-2.320.19862690.17774668X-RAY DIFFRACTION99.7
2.32-2.390.20272220.16864658X-RAY DIFFRACTION99.71
2.39-2.470.17852480.16764675X-RAY DIFFRACTION99.6
2.47-2.550.20192410.16934654X-RAY DIFFRACTION99.47
2.55-2.660.21432660.17794668X-RAY DIFFRACTION99.34
2.66-2.780.19812570.17834569X-RAY DIFFRACTION98.61
2.78-2.920.21942480.1844452X-RAY DIFFRACTION94.89
2.92-3.110.20252530.1824630X-RAY DIFFRACTION99.67
3.11-3.350.22762530.18024712X-RAY DIFFRACTION99.96
3.35-3.680.16642620.1594711X-RAY DIFFRACTION99.94
3.68-4.220.13892320.13234701X-RAY DIFFRACTION99.56
4.22-5.310.1322420.1184670X-RAY DIFFRACTION98.46
5.31-37.950.19082470.1694756X-RAY DIFFRACTION98.35
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.423859923470.158113208587-0.00131105588820.7957798334620.2259418307170.8908876639250.06473540867340.046389515625-0.0323562316193-0.1122947586790.041924644493-0.1051238435730.09623103387230.1127222540440.0036131409550.296077450490.04230676929650.01309128420250.253295462559-0.0168391480290.24524268765114.2034733868-22.898188862913.4743118596
20.6995171438550.1251524954020.1977507849340.7451437324470.3566353280390.9430278284540.0893940568417-0.1008979478150.11356630230.0922764552915-0.0839488949839-0.0009406885061320.00896699090908-0.0800075494495-0.0004537987818510.228542582898-0.02146247886350.02073215619290.261564262584-0.03278483012480.2580587413924.728179086450.31232080504744.3835891503
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'M' and resid 2 through 583)MU2 - 5831 - 582
22(chain 'A' and resid 3 through 583)AA3 - 5831 - 581

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