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8cqf

Crystal Structure of a Chimeric Alpha-Amylase from Pseudoalteromonas Haloplanktis Complexed with Rearranged Acarbose

Method: X-RAY DIFFRACTION Dmax: 78.3 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Alpha-amylase

Pseudoalteromonas haloplanktis

UniProt P29957

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 4 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 26–232 Chain A； UniProt 236–294 Chain A； UniProt 301–471 Mutation：A77V Q204L S226G T227A E228K N231T T232L G270_G271insA A272G G273S N274S V275I I276L D310N T311D D312W ;4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose ; × 2 ;4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-1,5-anhydro-D-glucitol ; × 1 ;alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose ; × 1 CL CHLORIDE ION × 2 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；3 M NaCl, 0.1 M BisTris Resolution 2.05 Å R-free 0.198

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 8CQF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AQH ALPHA-AMYLASE FROM ALTEROMONAS HALOPLANCTIS Deposited 1997-07-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 25–477（453 aa）
Not recorded CA CALCIUM ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；pH 7.0
Resolution 2.00 Å R-free 0.204
1AQM ALPHA-AMYLASE FROM ALTEROMONAS HALOPLANCTIS COMPLEXED WITH TRIS Deposited 1997-07-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 25–477（453 aa）
Not recorded CA CALCIUM ION × 1 CL CHLORIDE ION × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；pH 7.0
Resolution 1.85 Å R-free 0.186
1B0I ALPHA-AMYLASE FROM ALTEROMONAS HALOPLANCTIS Deposited 1998-11-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 25–477（453 aa）
Not recorded CA CALCIUM ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；pH 7.0
Resolution 2.40 Å R-free 0.217
1G94 CRYSTAL STRUCTURE ANALYSIS OF THE TERNARY COMPLEX BETWEEN PSYCHROPHILIC ALPHA AMYLASE FROM PSEUDOALTEROMONAS HALOPLANCTIS IN COMPLEX WITH A HEPTA-SACCHARIDE AND A TRIS MOLECULE Deposited 2000-11-22 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 25–472（448 aa）
Not recorded CA CALCIUM ION × 1 CL CHLORIDE ION × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；MPD, Hepes, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 1.74 Å R-free 0.187
1G9H TERNARY COMPLEX BETWEEN PSYCHROPHILIC ALPHA-AMYLASE, COMII (PSEUDO TRI-SACCHARIDE FROM BAYER) AND TRIS (2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL) Deposited 2000-11-23 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 25–472（448 aa）
Not recorded CA CALCIUM ION × 1 CL CHLORIDE ION × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；MPD, Hepes, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.80 Å R-free 0.201
1JD7 CRYSTAL STRUCTURE ANALYSIS OF THE MUTANT K300R OF PSEUDOALTEROMONAS HALOPLANCTIS ALPHA-AMYLASE Deposited 2001-06-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 25–477（453 aa）
Mutation：K300R CA CALCIUM ION × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；MPD, Hepes, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.25 Å R-free 0.215
1JD9 CRYSTAL STRUCTURE ANALYSIS OF THE MUTANT K300Q OF PSEUDOALTEROMONAS HALOPLANCTIS ALPHA-AMYLASE Deposited 2001-06-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 25–477（453 aa）
Mutation：K300Q CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；MPD, Hepes, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.50 Å R-free 0.245
1KXH Crystal structure of the complex between an inactive mutant of psychrophilic alpha-amylase (D174N) and acarbose Deposited 2002-01-31 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 25–472（448 aa）
Mutation：D174N CA CALCIUM ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；MPD, hepes, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.188
1L0P CRYSTAL STRUCTURE ANALYSIS OF THE COMPLEX BETWEEN PSYCHROPHILIC ALPHA AMYLASE FROM PSEUDOALTEROMONAS HALOPLANCTIS AND NITRATE Deposited 2002-02-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 25–472（448 aa）
Not recorded CA CALCIUM ION × 1 NO3 NITRATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；MPD, Hepes, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.10 Å R-free 0.180
8CQG Crystal Structure of a Chimeric Alpha-Amylase from Pseudoalteromonas Haloplanktis Deposited 2023-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 25–232（208 aa）
Chain A 236–294（59 aa）
Chain A 302–471（170 aa）
Mutation：A77V Q204L S226G T227A E228K N231T T232L G270_G271insA A272G G273S N274S V275I I276L D310N T311D D312W Mutation：A77V Q204L S226G T227A E228K N231T T232L G270_G271insA A272G G273S N274S V275I I276L D310N T311D D312W Mutation：A77V Q204L S226G T227A E228K N231T T232L G270_G271insA A272G G273S N274S V275I I276L D310N T311D D312W EDO 1,2-ETHANEDIOL × 11 CL CHLORIDE ION × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；3 M NaCl, 0.1 M BisTris
Resolution 1.74 Å R-free 0.205

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AMY_PSEHA
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–208； UniProt 26–232 Author chain A； PDBConstruct 212–270； UniProt 236–294 Author chain A； PDBConstruct 278–448； UniProt 301–471

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 8cqf

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id8cqf
Deposition date deposition_date2023-03-06
Structure title titleCrystal Structure of a Chimeric Alpha-Amylase from Pseudoalteromonas Haloplanktis Complexed with Rearranged Acarbose
Keywords keywordsInhibitor, Alpha-Amylase, Hydrolase, Chimeric; HYDROLASE
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_guinier23.56 Å
Radius of gyration Rg (electron density) rg_electron22.43 Å
Forward intensity I(0) i048158400.00
Molecular weight molecular_weight51770.0 kDa
Excluded volume excluded_volume63644 ų
Envelope volume envelope_volume71121 ų
Hydration-shell volume shell_volume26408 ų
Envelope diameter envelope_diameter80.7 Å
Shell Rg shell_rg29.72 Å
Envelope Rg envelope_rg22.69 Å
Shape Rg shape_rg22.39 Å
Total Rg total_rg23.30 Å
Total atoms total_atoms7021
Residues n_residues448
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 dmax78.3 Å
Rg (real space) rg_real23.54 Å
Rg uncertainty (real space) rg_real_error0.55 Å
I(0) (real space) i0_real4.8160e+07
I(0) uncertainty (real space) i0_real_error6.8180e+05
Rg (reciprocal space) rg_reciprocal23.55 Å
I(0) (reciprocal space) i0_reciprocal48160000.0000
Solution quality estimate total_estimate0.6072
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.1 Å
Skewness Skewness skewness0.385
Kurtosis Kurtosis kurtosis-0.195
Angular range angular_range— – 0.3350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9755000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.812; Stabil: 0.999; Sysdev: 0.154; Positv: 1.000; Valcen: 0.993; Smooth: 0.000
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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) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id8cqfA01
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
Domain ID domain_id8cqfA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1180 — Golgi alpha-mannosidase II
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8. Citations (1)

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9. Files and Curves (10)