SAXSdb — 1c9u

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

SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE

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 25–478 Chain B； UniProt 25–478	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

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 1C9U	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CQ1 Soluble Quinoprotein Glucose Dehydrogenase from Acinetobacter Calcoaceticus in Complex with PQQH2 and Glucose Deposited 1999-08-04	Different ligand/ion 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 ligand/ion 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 ligand/ion 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
5MIN Apo form of the soluble PQQ-dependent Glucose Dehydrogenase from Acinetobacter calcoaceticus Deposited 2016-11-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 25–477（453 aa） Chain B 25–477（453 aa）	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
8RE0 Soluble glucose dehydrogenase from acinetobacter calcoaceticus - double mutant pH8 Deposited 2023-12-09	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 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 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 1–454； UniProt 25–478 Author chain B； PDBConstruct 1–454； UniProt 25–478

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	1c9u
Deposition date deposition_date	1999-08-03
Structure title title	CRYSTAL STRUCTURE OF THE SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE IN COMPLEX WITH PQQ
Keywords keywords	BETA-PROPELLER, SUPERBARREL, COFACTOR BINDING, 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	29.80 Å
Radius of gyration Rg (electron density) rg_electron	29.05 Å
Forward intensity I(0) i0	157717000.00
Molecular weight molecular_weight	100350.0 kDa
Excluded volume excluded_volume	125760 Å³
Envelope volume envelope_volume	146460 Å³
Hydration-shell volume shell_volume	40841 Å³
Envelope diameter envelope_diameter	94.4 Å
Shell Rg shell_rg	37.26 Å
Envelope Rg envelope_rg	29.22 Å
Shape Rg shape_rg	29.02 Å
Total Rg total_rg	29.87 Å
Total atoms total_atoms	7086
Residues n_residues	896
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	93.9 Å
Rg (real space) rg_real	29.74 Å
Rg uncertainty (real space) rg_real_error	0.60 Å
I(0) (real space) i0_real	1.5770e+08
I(0) uncertainty (real space) i0_real_error	2.3910e+06
Rg (reciprocal space) rg_reciprocal	29.77 Å
I(0) (reciprocal space) i0_reciprocal	157700000.0000
Solution quality estimate total_estimate	0.9003
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.7 Å
Skewness Skewness skewness	0.280
Kurtosis Kurtosis kurtosis	-0.521
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	49740000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.923; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.929

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE
Molecular weight formula_weight	50293.2 kDa
EC 编号 ec_number	1.1.99.17
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	7634

DVPLTPSQFAKAKSENFDKKVILSNLNKPHALLWGPDNQIWLTERATGKILRVNPESGSVKTVFQVPEIVNDADGQNGLLGFAFHPDFKNNPYIYISGTFKNPKSTDKELPNQTIIRRYTYNKSTDTLEKPVDLLAGLPSSKDHQSGRLVIGPDQKIYYTIGDQGRNQLAYLFLPNQAQHTPTQQELNGKDYHTYMGKVLRLNLDGSIPKDNPSFNGVVSHIYTLGHRNPQGLAFTPNGKLLQSEQGPNSDDEINLIVKGGNYGWPNVAGYKDDSGYAYANYSAAANKSIKDLAQNGVKVAAGVPVTKESEWTGKNFVPPLKTLYTVQDTYNYNDPTCGEMTYICWPTVAPSSAYVYKGGKKAITGWENTLLVPSLKRGVIFRIKLDPTYSTTYDDAVPMFKSNNRYRDVIASPDGNVLYVLTDTAGNVQKDDGSVTNTLENPGSLIKFTYKAK

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

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	PYRROLOQUINOLINE QUINONE
Molecular weight formula_weight	330.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	548

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1c9ua_
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	d1c9ub_
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	1c9uA00
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	1c9uB00
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 (2)

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Unit-cell length a length_a	60.590 Å
Unit-cell length b length_b	158.720 Å
Unit-cell length c length_c	221.390 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2240
R_work r_work	0.2230
R_free r_free	0.2860

fit	/app/data/saxs_computation/c9/1c9u/1c9u.fit
pddf	/app/data/pr_computation/c9/1c9u/1c9u.pr.out
profile	/app/data/saxs_computation/c9/1c9u/1c9u.dat

CRYSTAL STRUCTURE OF THE SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE IN COMPLEX WITH PQQ

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

SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE

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