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3qvp

Crystal structure of glucose oxidase for space group C2221 at 1.2 A resolution

Method: X-RAY DIFFRACTION Dmax: 79.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Glucose oxidase

Aspergillus niger

UniProt P13006

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 23–605 Not recorded ;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 ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.9；295 K；200 mM NaCl and 20% PEG 3350, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 1.20 Å R-free 0.188

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3QVP Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CF3 GLUCOSE OXIDASE FROM APERGILLUS NIGER Deposited 1999-03-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–583（583 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；pH 5.6
Resolution 1.90 Å R-free 0.240
1GAL CRYSTAL STRUCTURE OF GLUCOSE OXIDASE FROM ASPERGILLUS NIGER: REFINED AT 2.3 ANGSTROMS RESOLUTION Deposited 1992-08-27 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 23–605（583 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å
3QVR Crystal structure of glucose oxidase for space group P3121 at 1.3 A resolution. Deposited 2011-02-25 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 23–605（583 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.1；295 K；200 mM CaCl2 and 20% PEG 3350, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.30 Å R-free 0.198
5NIT Glucose oxidase mutant A2 Deposited 2017-03-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 25–605（581 aa）
Mutation：T30V I94V A162T R537K M556V FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 OXY OXYGEN MOLECULE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 DIO 1,4-DIETHYLENE DIOXIDE × 18 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；280 K；100 mM HEPES 40% v/v dioxane
Resolution 1.87 Å R-free 0.204
5NIW Glucose oxydase mutant A2 Deposited 2017-03-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 25–605（581 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 OXY OXYGEN MOLECULE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 DIO 1,4-DIETHYLENE DIOXIDE × 12 PEG DI(HYDROXYETHYL)ETHER × 2 P4C O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；280 K；100 mM HEPES 45% v/v dioxane
Resolution 1.80 Å R-free 0.191
9H7Z Aspergillus niger Glucose Oxidase bound to Ba2+ ions Deposited 2024-10-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–605（605 aa）
Chain M 1–605（605 aa）
Not recorded EDO 1,2-ETHANEDIOL × 6 MAN alpha-D-mannopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 CL CHLORIDE ION × 10 NA SODIUM ION × 6 BA BARIUM ION × 12 BR BROMIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.8；298 K；20% PEG 4000, 0.2 M sodium bromide, 2 mM barium chloride, 30 mM sodium acetate
Resolution 1.71 Å R-free 0.199

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GOX_ASPNG
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–583； UniProt 23–605

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 3qvp

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3qvp
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3qvp
Deposition date deposition_date2011-02-25
Structure title titleCrystal structure of glucose oxidase for space group C2221 at 1.2 A resolution
Keywords keywordsOXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier24.42 Å
Radius of gyration Rg (electron density) rg_electron23.31 Å
Forward intensity I(0) i074265300.00
Molecular weight molecular_weight65573.0 kDa
Excluded volume excluded_volume81100 ų
Envelope volume envelope_volume92529 ų
Hydration-shell volume shell_volume31705 ų
Envelope diameter envelope_diameter83.0 Å
Shell Rg shell_rg31.76 Å
Envelope Rg envelope_rg23.77 Å
Shape Rg shape_rg23.28 Å
Total Rg total_rg24.28 Å
Total atoms total_atoms4622
Residues n_residues581
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax79.4 Å
Rg (real space) rg_real24.29 Å
Rg uncertainty (real space) rg_real_error0.42 Å
I(0) (real space) i0_real7.4270e+07
I(0) uncertainty (real space) i0_real_error9.3330e+05
Rg (reciprocal space) rg_reciprocal24.32 Å
I(0) (reciprocal space) i0_reciprocal74270000.0000
Solution quality estimate total_estimate0.8837
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.2 Å
Skewness Skewness skewness0.249
Kurtosis Kurtosis kurtosis-0.339
Angular range angular_range— – 0.3250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha26660000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.835; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.980
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3qvpa1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamilyc.3.1 — FAD/NAD(P)-binding domain
Family Family familyc.3.1.2 — FAD-linked reductases, N-terminal domain
Domain ID domain_idd3qvpa2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.16 — FAD-linked reductases, C-terminal domain
Superfamily Superfamily superfamilyd.16.1 — FAD-linked reductases, C-terminal domain
Family Family familyd.16.1.1 — GMC oxidoreductases

CATH v4.4 (3 domains)

Domain ID domain_id3qvpA01
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily60 — FAD/NAD(P)-binding domain
Domain ID domain_id3qvpA02
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology450 — Glucose Oxidase; domain 2
Homologous superfamily homologous superfamily10 — Glucose Oxidase, domain 2
Domain ID domain_id3qvpA03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology560 — Glucose Oxidase; domain 3
Homologous superfamily homologous superfamily10 — Glucose Oxidase, domain 3
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8. Citations (2)

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9. Files and Curves (10)