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8rfk

Soluble glucose dehydrogenase from acinetobacter calcoaceticus - single mutant pH8

Method: X-RAY DIFFRACTION Dmax: 95.5 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Quinoprotein glucose dehydrogenase B

Acinetobacter calcoaceticus

UniProt P13650

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 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

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 8RFK 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 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）
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 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）
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 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）
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 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）
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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 25–477（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 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）
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
8RG1 Soluble glucose dehydrogenase from acinetobacter calcoaceticus - wild type 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）
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.

SAXS scattering curve SAXS Profile

SAXS profile for 8rfk

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8rfk
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8rfk
Deposition date deposition_date2023-12-13
Structure title titleSoluble glucose dehydrogenase from acinetobacter calcoaceticus - single mutant pH8
Keywords keywordsDouble point mutation, OXIDOREDUCTASE; 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_guinier30.03 Å
Radius of gyration Rg (electron density) rg_electron29.27 Å
Forward intensity I(0) i0159703000.00
Molecular weight molecular_weight100990.0 kDa
Excluded volume excluded_volume126540 ų
Envelope volume envelope_volume150290 ų
Hydration-shell volume shell_volume41499 ų
Envelope diameter envelope_diameter96.9 Å
Shell Rg shell_rg37.62 Å
Envelope Rg envelope_rg29.51 Å
Shape Rg shape_rg29.24 Å
Total Rg total_rg30.11 Å
Total atoms total_atoms14090
Residues n_residues904
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 dmax95.5 Å
Rg (real space) rg_real29.97 Å
Rg uncertainty (real space) rg_real_error0.50 Å
I(0) (real space) i0_real1.5970e+08
I(0) uncertainty (real space) i0_real_error2.1720e+06
Rg (reciprocal space) rg_reciprocal30.00 Å
I(0) (reciprocal space) i0_reciprocal159700000.0000
Solution quality estimate total_estimate0.9002
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.2 Å
Skewness Skewness skewness0.280
Kurtosis Kurtosis kurtosis-0.514
Angular range angular_range— – 0.2650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha52360000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.960
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (1)

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9. Files and Curves (10)