SAXSdb — 5min

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

Quinoprotein glucose dehydrogenase B

Acinetobacter calcoaceticus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 25–477 Chain B； UniProt 25–477	Not recorded	CA CALCIUM ION × 6 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；PEG 4000 (12%) 100 mM TRIS pH 8.5	Resolution 1.76 Å R-free 0.214

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 5MIN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C9U CRYSTAL STRUCTURE OF THE SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE IN COMPLEX WITH PQQ Deposited 1999-08-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 25–478（454 aa） Chain B 25–478（454 aa）	Not recorded	CA CALCIUM ION × 6 PQQ PYRROLOQUINOLINE QUINONE × 2 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.2；293 K；PEG 6000, SODIUM CHLORIDE, CALCIUM CHLORIDE, TRIS, GLYCINE, pH 9.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.286
1CQ1 Soluble Quinoprotein Glucose Dehydrogenase from Acinetobacter Calcoaceticus in Complex with PQQH2 and Glucose Deposited 1999-08-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 25–478（454 aa） Chain B 25–478（454 aa）	Not recorded	BGC beta-D-glucopyranose × 2 CA CALCIUM ION × 6 PQQ PYRROLOQUINOLINE QUINONE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.2；293 K；PEG 6000, SODIUM CHLORIDE, CALCIUM CHLORIDE, TRIS, GLYCINE, pH 9.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.226
1CRU SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE FROM ACINETOBACTER CALCOACETICUS IN COMPLEX WITH PQQ AND METHYLHYDRAZINE Deposited 1999-08-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 25–478（454 aa） Chain B 25–478（454 aa）	Not recorded	CA CALCIUM ION × 6 PQQ PYRROLOQUINOLINE QUINONE × 2 HDN METHYLHYDRAZINE × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.2；293 K；PEG 6000, SODIUM CHLORIDE, CALCIUM CHLORIDE, TRIS, GLYCINE, pH 9.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.50 Å R-free 0.195
1QBI SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE FROM ACINETOBACTER CALCOACETICUS Deposited 1999-04-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 25–478（454 aa） Chain B 25–478（454 aa）	Not recorded	PT PLATINUM (II) ION × 2 CA CALCIUM ION × 6 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.2；293 K；PEG 6000, SODIUM CHLORIDE, CALCIUM CHLORIDE, TRIS, GLYCINE, pH 9.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.72 Å R-free 0.208
8RE0 Soluble glucose dehydrogenase from acinetobacter calcoaceticus - double mutant pH8 Deposited 2023-12-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 25–478（454 aa） Chain B 25–478（454 aa）	Not recorded	CA CALCIUM ION × 6 A1H0D 3-(3,5-dicarboxy-1~{H}-pyrrol-2-yl)pyridine-2,4,6-tricarboxylic acid × 2 LI LITHIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；20% PEG 6000, 100mM TRIS pH8, 200 mM LiCl2	Resolution 1.56 Å R-free 0.183
8RFK Soluble glucose dehydrogenase from acinetobacter calcoaceticus - single mutant pH8 Deposited 2023-12-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 25–478（454 aa） Chain B 25–478（454 aa）	Mutation：D143E,Y343F Mutation：D143E,Y343F	CA CALCIUM ION × 6 A1H0D 3-(3,5-dicarboxy-1~{H}-pyrrol-2-yl)pyridine-2,4,6-tricarboxylic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；300 K；PEG 6000, TRIS, Lithium chloride	Resolution 1.56 Å R-free 0.185
8RG1 Soluble glucose dehydrogenase from acinetobacter calcoaceticus - wild type pH8 Deposited 2023-12-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 25–478（454 aa） Chain B 25–478（454 aa）	Not recorded	A1H0D 3-(3,5-dicarboxy-1~{H}-pyrrol-2-yl)pyridine-2,4,6-tricarboxylic acid × 2 CA CALCIUM ION × 6 LI LITHIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；PEG 6000, 100 mM TRIS pH8, 2 mM ZnCl2	Resolution 1.19 Å R-free 0.173

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DHGB_ACICA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–453； UniProt 25–477 Author chain B； PDBConstruct 1–453； UniProt 25–477

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5min
Deposition date deposition_date	2016-11-28
Structure title title	Apo form of the soluble PQQ-dependent Glucose Dehydrogenase from Acinetobacter calcoaceticus
Keywords keywords	Dehydrogenase, Apo form, 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	30.16 Å
Radius of gyration Rg (electron density) rg_electron	29.38 Å
Forward intensity I(0) i0	156705000.00
Molecular weight molecular_weight	100280.0 kDa
Excluded volume excluded_volume	125820 Å³
Envelope volume envelope_volume	151600 Å³
Hydration-shell volume shell_volume	41734 Å³
Envelope diameter envelope_diameter	96.4 Å
Shell Rg shell_rg	37.64 Å
Envelope Rg envelope_rg	29.58 Å
Shape Rg shape_rg	29.35 Å
Total Rg total_rg	30.23 Å
Total atoms total_atoms	7080
Residues n_residues	905
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	95.0 Å
Rg (real space) rg_real	30.09 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	1.5670e+08
I(0) uncertainty (real space) i0_real_error	2.2410e+06
Rg (reciprocal space) rg_reciprocal	30.13 Å
I(0) (reciprocal space) i0_reciprocal	156700000.0000
Solution quality estimate total_estimate	0.9009
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.0 Å
Skewness Skewness skewness	0.277
Kurtosis Kurtosis kurtosis	-0.515
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	53220000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.942

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Quinoprotein glucose dehydrogenase B
Molecular weight formula_weight	50106.0 kDa
EC 编号 ec_number	1.1.5.2
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	8241

DVPLTPSQFAKAKSENFDKKVILSNLNKPHALLWGPDNQIWLTERATGKILRVNPESGSVKTVFQVPEIVNDADGQNGLLGFAFHPDFKNNPYIYISGTFKNPKSTDKALPNQTIIRRYTYNKSTDTLEKPVDLLAGLPSSKDHQSGRLVIGPDQKIYYTIGDQGRNQLAYLFLPNQAQHTPTQQELNGKDYHTYMGKVLRLNLDGSIPKDNPSFNGVVSHIYTLGHRNPQGLAFTPNGKLLQSEQGPNSDDEINLIVKGGNYGWPNVAGYKDDSGYAYANYSAAANKSIKDLAQNGVKVAAGVPVTKESEWTGKNFVPPLKTLYTVQDTYNYNDPTCGEMTYICWPTVAPSSAYVYKGGKKAITGWENTLLVPSLKRGVIFRIKLDPTYSTTYDDAVPMFKSNNRYRDVIASPDGNVLYVLTDTAGNVQKDDGSVTNTLENPGSLIKFTYKA

来源 Source

来源生物 organism	Acinetobacter calcoaceticus
NCBI Class编号 ncbi_taxonomy_id	471
宿主生物 host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1099

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5mina_
Class class	b — All beta proteins
Fold Fold fold	b.68 — 6-bladed beta-propeller
Superfamily Superfamily superfamily	b.68.2 — Soluble quinoprotein glucose dehydrogenase
Family Family family	b.68.2.1 — Soluble quinoprotein glucose dehydrogenase

Domain ID domain_id	d5minb_
Class class	b — All beta proteins
Fold Fold fold	b.68 — 6-bladed beta-propeller
Superfamily Superfamily superfamily	b.68.2 — Soluble quinoprotein glucose dehydrogenase
Family Family family	b.68.2.1 — Soluble quinoprotein glucose dehydrogenase

CATH v4.4 (2 domains)

Domain ID domain_id	5minA00
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	30 — TolB, C-terminal domain

Domain ID domain_id	5minB00
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	30 — TolB, C-terminal domain

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8. Citations (1)

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Unit-cell length a length_a	54.407 Å
Unit-cell length b length_b	54.898 Å
Unit-cell length c length_c	85.474 Å
Unit-cell angle α angle_alpha	88.04 °
Unit-cell angle β angle_beta	81.58 °
Unit-cell angle γ angle_gamma	69.62 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	1.760 Å
Low-resolution limit resolution_low	25.730 Å
R factor r_factor	0.1795
R_work r_work	0.1776
R_free r_free	0.2144

fit	/app/data/saxs_computation/mi/5min/5min.fit
pddf	/app/data/pr_computation/mi/5min/5min.pr.out
profile	/app/data/saxs_computation/mi/5min/5min.dat

Apo form of the soluble PQQ-dependent Glucose Dehydrogenase from Acinetobacter calcoaceticus

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

Quinoprotein glucose dehydrogenase B

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction