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1e3x

Native structure of chimaeric amylase from B. amyloliquefaciens and B. licheniformis at 1.92A

Method: X-RAY DIFFRACTION Dmax: 86.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

ALPHA-AMYLASE

BACILLUS AMYLOLIQUEFACIENS

UniProt P00692

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 32–331 Not recorded CA CALCIUM ION × 4 NA SODIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；CRYSTALS WERE GROWN AT 18C USING THE HANGING DROP METHOD WITH 8-13% MONOMETHYL ETHER POLYETHYLENE GLYCOL 2000 OR 5000 AS PRECIPITANT. DROPS WERE BUFFERED WITH 0.1M TRIS/HCL PH 7.5 CONTAINING 5MM CACL2 AND THE PROTEIN CONCENTRATION WAS 30-35MG/ML. Resolution 1.90 Å R-free 0.200

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 1E3X Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1E3Z Acarbose complex of chimaeric amylase from B. amyloliquefaciens and B. licheniformis at 1.93A Deposited 2000-06-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–331（300 aa）
Not recorded CA CALCIUM ION × 4 NA SODIUM ION × 1 ACI 6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；CRYSTALS WERE GROWN AT 18C USING THE HANGING DROP METHOD WITH 8-13% MONOMETHYL ETHER POLYETHYLENE GLYCOL 2000 OR 5000 AS PRECIPITANT. DROPS WERE BUFFERED WITH 0.1M TRIS/HCL PH 7.5 CONTAINING 5MM CACL2 AND THE PROTEIN CONCENTRATION WAS 30-35MG/ML. CRYSTALS WERE THEN SOAKED IN 10MM ACARBOSE SOLUTION TO OBTAIN THE COMPLEX.
Resolution 1.93 Å R-free 0.200
1E40 Tris/maltotriose complex of chimaeric amylase from B. amyloliquefaciens and B. licheniformis at 2.2A Deposited 2000-06-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–331（300 aa）
Not recorded CA CALCIUM ION × 4 NA SODIUM ION × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；CRYSTALS WERE GROWN AT 18C USING THE HANGING DROP METHOD WITH 8-13% MONOMETHYL ETHER POLYETHYLENE GLYCOL 2000 OR 5000 AS PRECIPITANT. DROPS WERE BUFFERED WITH 0.1M TRIS/HCL PH 7.5 CONTAINING 5MM CACL2 AND THE PROTEIN CONCENTRATION WAS 30-35MG/ML. CRYSTALS WERE THEN SOAKED IN 10MM MALTOTRIOSE SOLUTION TO OBTAIN THE COMPLEX.
Resolution 2.20 Å R-free 0.210
1E43 Native structure of chimaeric amylase from B. amyloliquefaciens and B. licheniformis at 1.7A Deposited 2000-06-27 Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–331（300 aa）
Not recorded CA CALCIUM ION × 4 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10；291 K；CRYSTALS WERE GROWN AT 18C USING THE HANGING DROP METHOD WITH 8-13% MONOMETHYL ETHER POLYETHYLENE GLYCOL 2000 OR 5000 AS PRECIPITANT. DROPS WERE BUFFERED WITH 0.1M TRIS/HCL PH 7.5 CONTAINING 5MM CACL2 AND THE PROTEIN CONCENTRATION WAS 30-35MG/ML.
Resolution 1.70 Å R-free 0.185
3BH4 High resolution crystal structure of Bacillus amyloliquefaciens alpha-amylase Deposited 2007-11-28 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–514（483 aa）
Not recorded CA CALCIUM ION × 4 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；100mM Tris-HCl, pH7.5, 24% PEG3350, 3.5mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.40 Å R-free 0.219
3BH4 High resolution crystal structure of Bacillus amyloliquefaciens alpha-amylase Deposited 2007-11-28 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 32–514（483 aa）
Not recorded CA CALCIUM ION × 4 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；100mM Tris-HCl, pH7.5, 24% PEG3350, 3.5mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.40 Å R-free 0.219

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AMY_BACAM
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–300； UniProt 32–331

ALPHA-AMYLASE

BACILLUS AMYLOLIQUEFACIENS

UniProt P06278

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 330–512 Not recorded CA CALCIUM ION × 4 NA SODIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；CRYSTALS WERE GROWN AT 18C USING THE HANGING DROP METHOD WITH 8-13% MONOMETHYL ETHER POLYETHYLENE GLYCOL 2000 OR 5000 AS PRECIPITANT. DROPS WERE BUFFERED WITH 0.1M TRIS/HCL PH 7.5 CONTAINING 5MM CACL2 AND THE PROTEIN CONCENTRATION WAS 30-35MG/ML. Resolution 1.90 Å R-free 0.200

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 1E3X Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BLI BACILLUS LICHENIFORMIS ALPHA-AMYLASE Deposited 1998-01-07 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 30–512（483 aa）
Mutation：N190F, Q264S, N265Y CA CALCIUM ION × 3 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；pH 7.0
Resolution 1.90 Å R-free 0.185
1BPL GLYCOSYLTRANSFERASE Deposited 1995-07-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 30–218（189 aa）
Chain B 219–512（294 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.2；MOLECULE: ALPHA-1,4-GLUCAN-4-GLUCANOHYDROLASE FROM BACILLUS LICHENIFORMIS. VAPOR DIFFUSION, ROOM TEMPERATURE PROTEIN SOLUTION: 15 MG/ML BLA IN 0.4 M SODIUM CITRATE 2.5 MM EDTA, PH 8.2 RESERVOIR: 0.66 M SODIUM CITRATE, 2.5 MM EDTA, PH 8.2 CALCIUM REMOVAL BY EDTA LEADS TO A CLEAVAGE OF BLA AFTER GLU 189 DUE TO TRACE AMOUNTS OF A GLU-C-ENDOPEPTIDASE PRESENT IN THE PREPARATION (SEE PAPER)., vapor diffusion
Resolution 2.20 Å
1E3Z Acarbose complex of chimaeric amylase from B. amyloliquefaciens and B. licheniformis at 1.93A Deposited 2000-06-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 330–512（183 aa）
Not recorded CA CALCIUM ION × 4 NA SODIUM ION × 1 ACI 6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；CRYSTALS WERE GROWN AT 18C USING THE HANGING DROP METHOD WITH 8-13% MONOMETHYL ETHER POLYETHYLENE GLYCOL 2000 OR 5000 AS PRECIPITANT. DROPS WERE BUFFERED WITH 0.1M TRIS/HCL PH 7.5 CONTAINING 5MM CACL2 AND THE PROTEIN CONCENTRATION WAS 30-35MG/ML. CRYSTALS WERE THEN SOAKED IN 10MM ACARBOSE SOLUTION TO OBTAIN THE COMPLEX.
Resolution 1.93 Å R-free 0.200
1E40 Tris/maltotriose complex of chimaeric amylase from B. amyloliquefaciens and B. licheniformis at 2.2A Deposited 2000-06-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 330–512（183 aa）
Not recorded CA CALCIUM ION × 4 NA SODIUM ION × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；CRYSTALS WERE GROWN AT 18C USING THE HANGING DROP METHOD WITH 8-13% MONOMETHYL ETHER POLYETHYLENE GLYCOL 2000 OR 5000 AS PRECIPITANT. DROPS WERE BUFFERED WITH 0.1M TRIS/HCL PH 7.5 CONTAINING 5MM CACL2 AND THE PROTEIN CONCENTRATION WAS 30-35MG/ML. CRYSTALS WERE THEN SOAKED IN 10MM MALTOTRIOSE SOLUTION TO OBTAIN THE COMPLEX.
Resolution 2.20 Å R-free 0.210
1E43 Native structure of chimaeric amylase from B. amyloliquefaciens and B. licheniformis at 1.7A Deposited 2000-06-27 Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 330–512（183 aa）
Not recorded CA CALCIUM ION × 4 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10；291 K；CRYSTALS WERE GROWN AT 18C USING THE HANGING DROP METHOD WITH 8-13% MONOMETHYL ETHER POLYETHYLENE GLYCOL 2000 OR 5000 AS PRECIPITANT. DROPS WERE BUFFERED WITH 0.1M TRIS/HCL PH 7.5 CONTAINING 5MM CACL2 AND THE PROTEIN CONCENTRATION WAS 30-35MG/ML.
Resolution 1.70 Å R-free 0.185
1OB0 Kinetic stabilization of Bacillus licheniformis alpha-amylase through introduction of hydrophobic residues at the surface Deposited 2003-01-21 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 30–512（483 aa）
Mutation：YES CA CALCIUM ION × 3 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；PROTEIN WAS CRYSTALLIZED BY VAPOR DIFFUSION FROM DROPS CONTAINING 4 UL OF PROTEIN SOLUTION (10 MG/ML IN 50 MM TRIS/HCL, PH 8.0) PLUS 4 UL OF RESERVOIR SOLUTION (50 MM HEPES, 1 M AMMONIUM SULFATE, 1% (V/V) PEG 500, PH 7.0) EQUILIBRATED AGAINST 1 ML OF RESERVOIR SOLUTION.
Resolution 1.83 Å R-free 0.154
1VJS STRUCTURE OF ALPHA-AMYLASE PRECURSOR Deposited 1996-10-02 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 30–512（483 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.70 Å R-free 0.226

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

View Construct and Data Evidence
UniProt name AMY_BACLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 301–483； UniProt 330–512

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 1e3x

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1e3x
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1e3x
Deposition date deposition_date2000-06-26
Structure title titleNative structure of chimaeric amylase from B. amyloliquefaciens and B. licheniformis at 1.92A
Keywords keywordsHYDROLASE, AMYLASE, FAMILY 13; 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_guinier25.59 Å
Radius of gyration Rg (electron density) rg_electron24.48 Å
Forward intensity I(0) i051961800.00
Molecular weight molecular_weight55142.0 kDa
Excluded volume excluded_volume68324 ų
Envelope volume envelope_volume78810 ų
Hydration-shell volume shell_volume27524 ų
Envelope diameter envelope_diameter89.2 Å
Shell Rg shell_rg31.38 Å
Envelope Rg envelope_rg24.63 Å
Shape Rg shape_rg24.46 Å
Total Rg total_rg25.25 Å
Total atoms total_atoms3905
Residues n_residues483
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 dmax86.2 Å
Rg (real space) rg_real25.64 Å
Rg uncertainty (real space) rg_real_error0.73 Å
I(0) (real space) i0_real5.1960e+07
I(0) uncertainty (real space) i0_real_error8.3710e+05
Rg (reciprocal space) rg_reciprocal25.63 Å
I(0) (reciprocal space) i0_reciprocal51960000.0000
Solution quality estimate total_estimate0.8667
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary84.8 Å
Skewness Skewness skewness0.454
Kurtosis Kurtosis kurtosis-0.137
Angular range angular_range— – 0.3100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8483000.0000
Real-space data points n_real_points63
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.810; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.847
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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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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1e3xa1
Class classb — All beta proteins
Fold Fold foldb.71 — Glycosyl hydrolase domain
Superfamily Superfamily superfamilyb.71.1 — Glycosyl hydrolase domain
Family Family familyb.71.1.1 — alpha-Amylases, C-terminal beta-sheet domain
Domain ID domain_idd1e3xa2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.8 — (Trans)glycosidases
Family Family familyc.1.8.1 — Amylase, catalytic domain

CATH v4.4 (3 domains)

Domain ID domain_id1e3xA01
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
Domain ID domain_id1e3xA02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily140 —
Domain ID domain_id1e3xA03
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)