9h7z

Aspergillus niger Glucose Oxidase bound to Ba2+ ions

Method: X-RAY DIFFRACTION D_max: 95.8 Å Quality: EXCELLENT

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Glucose oxidase

OrganismNot specified

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 Homooligomer Protein × 2 其他Polymer 7 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–605 Chain M； UniProt 1–605	Not recorded	;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 ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ;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 ; × 1 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

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 9H7Z	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 mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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
3QVP Crystal structure of glucose oxidase for space group C2221 at 1.2 A resolution Deposited 2011-02-25	Different construct Different mutation/modification Different oligomeric state 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 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
3QVR Crystal structure of glucose oxidase for space group P3121 at 1.3 A resolution. Deposited 2011-02-25	Different construct Different mutation/modification Different oligomeric state 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 oligomeric state 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 mutation/modification Different oligomeric state 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

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 1–605； UniProt 1–605 Author chain M； PDBConstruct 1–605； UniProt 1–605

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9h7z
Deposition date deposition_date	2024-10-28
最后修订 last_revision	2025-11-05
Structure title title	Aspergillus niger Glucose Oxidase bound to Ba2+ ions
Keywords keywords	Oxidoreductase; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	31.83 Å
Radius of gyration Rg (electron density) rg_electron	30.74 Å
Forward intensity I(0) i0	310624000.00
Molecular weight molecular_weight	135810.0 kDa
Excluded volume excluded_volume	166590 Å³
Envelope volume envelope_volume	196770 Å³
Hydration-shell volume shell_volume	50542 Å³
Envelope diameter envelope_diameter	100.0 Å
Shell Rg shell_rg	40.08 Å
Envelope Rg envelope_rg	30.65 Å
Shape Rg shape_rg	30.69 Å
Total Rg total_rg	31.57 Å
Total atoms total_atoms	18286
Residues n_residues	1163
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	95.8 Å
Rg (real space) rg_real	31.62 Å
Rg uncertainty (real space) rg_real_error	0.45 Å
I(0) (real space) i0_real	3.1060e+08
I(0) uncertainty (real space) i0_real_error	4.2040e+06
Rg (reciprocal space) rg_reciprocal	31.72 Å
I(0) (reciprocal space) i0_reciprocal	310600000.0000
Solution quality estimate total_estimate	0.9111
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	38.3 Å
Skewness Skewness skewness	0.118
Kurtosis Kurtosis kurtosis	-0.613
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	108000000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.960; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.975

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (13)

Entity 1 Entity 1 polymer

Description description	Glucose oxidase
Molecular weight formula_weight	65695.9 kDa
EC 编号 ec_number	1.1.3.4
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,M
Atom count atom_count	19052

MQTLLVSSLVVSLAAALPHYIRSNGIEASLLTDPKDVSGRTVDYIIAGGGLTGLTTAARLTENPNISVLVIESGSYESDRGPIIEDLNAYGDIFGSSVDHAYETVELATNNQTALIRSGNGLGGSTLVNGGTWTRPHKAQVDSWETVFGNEGWNWDNVAAYSLQAERARAPNAKQIAAGHYFNASCHGVNGTVHAGPRDTGDDYSPIVKALMSAVEDRGVPTKKDFGCGDPHGVSMFPNTLHEDQVRSDAAREWLLPNYQRPNLQVLTGQYVGKVLLSQNGTTPRAVGVEFGTHKGNTHNVYAKHEVLLAAGSAVSPTILEYSGIGMKSILEPLGIDTVVDLPVGLNLQDQTTATVRSRITSAGAGQGQAAWFATFNETFGDYSEKAHELLNTKLEQWAEEAVARGGFHNTTALLIQYENYRDWIVNHNVAYSELFLDTAGVASFDVWDLLPFTRGYVHILDKDPYLHHFAYDPQYFLNELDLLGQAAATQLARNISNSGAMQTYFAGETIPGDNLAYDADLSAWTEYIPYHFRPNYHGVGTCSMMPKEMGGVVDNAARVYGVQGLRVIDGSIPPTQMSSHVMTVFYAMALKISDAILEDYASMQ

Entity 2 Entity 2 branched

Description description	;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 ;
Molecular weight formula_weight	1073.0 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	5

Entity 4 Entity 4 branched

Description description	;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 ;
Molecular weight formula_weight	1397.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 non-polymer

Description description	alpha-D-mannopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 8 Entity 8 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 10 Entity 10 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 11 Entity 11 non-polymer

Description description	BARIUM ION
Molecular weight formula_weight	137.3 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 12 Entity 12 non-polymer

Description description	BROMIDE ION
Molecular weight formula_weight	79.9 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 13 Entity 13 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	664

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8. Citations (1)

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Unit-cell length a length_a	85.219 Å
Unit-cell length b length_b	82.251 Å
Unit-cell length c length_c	103.300 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.27 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	1.710 Å
Low-resolution limit resolution_low	37.950 Å
R factor r_factor	0.1777
R_work r_work	0.1766
R_free r_free	0.1989

fit	/app/data/saxs_computation/h7/9h7z/9h7z.fit
pddf	/app/data/pr_computation/h7/9h7z/9h7z.pr.out
profile	/app/data/saxs_computation/h7/9h7z/9h7z.dat