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- PDB-3qvr: Crystal structure of glucose oxidase for space group P3121 at 1.3... -

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Basic information

Entry
Database: PDB / ID: 3qvr
TitleCrystal structure of glucose oxidase for space group P3121 at 1.3 A resolution.
ComponentsGlucose oxidase
KeywordsOXIDOREDUCTASE
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
FLAVIN-ADENINE DINUCLEOTIDE / Glucose oxidase
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsKommoju, P. / Chen, Z. / Bruckner, R.C. / Mathews, F.S. / Jorns, M.S.
Citation
Journal: Biochemistry / Year: 2011
Title: Probing oxygen activation sites in two flavoprotein oxidases using chloride as an oxygen surrogate.
Authors: Kommoju, P.R. / Chen, Z.W. / Bruckner, R.C. / Mathews, F.S. / Jorns, M.S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: 1.8 and 1.9 A resolution structures of the Penicillium amagasakiense and Aspergillus niger glucose oxidases as a basis for modelling substrate complexes.
Authors: Wohlfahrt, G. / Witt, S. / Hendle, J. / Schomburg, D. / Kalisz, H.M. / Hecht, H.J.
History
DepositionFeb 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)65,7247
Polymers63,3291
Non-polymers2,3956
Water18,1951010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.952, 65.952, 214.252
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1190-

HOH

21A-1286-

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: 63329.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus niger (mold) / Gene: gox / References: UniProt: P13006, glucose oxidase

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Sugars , 2 types, 4 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-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: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: 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 , 3 types, 1012 molecules

#4: 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
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1010 / 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: 2.12 Å3/Da / Density % sol: 42.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: 200 mM CaCl2 and 20% PEG 3350, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 30, 2009
RadiationMonochromator: APS Biocars 14-BM-C / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.3→40 Å / Num. all: 133835 / Num. obs: 132764 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 11.3 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 29.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.3-1.325.40.3213.66534198.7
1.32-1.355.70.30546507198.9
1.35-1.375.80.2944.36575198.9
1.37-1.46.10.2764.76518199.1
1.4-1.436.20.265.26570199.1
1.43-1.466.60.2336.16591199.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPfrom ccp4phasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1CF3

1cf3


Resolution: 1.3→20.06 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 185564.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.198 6736 5.1 %RANDOM
Rwork0.18 ---
obs0.18 132723 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 71.0845 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 17.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20 Å20 Å2
2--0.96 Å20 Å2
3----1.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.3→20.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4452 0 157 1010 5619
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d1.13
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_mcangle_it1.672
X-RAY DIFFRACTIONc_scbond_it2.162
X-RAY DIFFRACTIONc_scangle_it3.022.5
LS refinement shellResolution: 1.3→1.38 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.331 1072 5 %
Rwork0.318 20565 -
obs-20565 98.4 %

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