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1bpl

GLYCOSYLTRANSFERASE

Method: X-RAY DIFFRACTION Dmax: 84.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

ALPHA-1,4-GLUCAN-4-GLUCANOHYDROLASE

OrganismNot specified

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 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 30–218 Chain B； UniProt 219–512 Not recorded No other associated polymer 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

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 1BPL 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
1E3X Native structure of chimaeric amylase from B. amyloliquefaciens and B. licheniformis at 1.92A Deposited 2000-06-26 Different construct Different mutation/modification 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 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
1E3Z Acarbose complex of chimaeric amylase from B. amyloliquefaciens and B. licheniformis at 1.93A Deposited 2000-06-27 Different construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 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 mutation/modification Different oligomeric state 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, 2
Chains and sequence ranges Author chain A； PDBConstruct 1–189； UniProt 30–218 Author chain B； PDBConstruct 1–294； UniProt 219–512

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 1bpl

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1bpl
Deposition date deposition_date1995-07-13
Structure title titleGLYCOSYLTRANSFERASE
Keywords keywordsALPHA-1, 4-GLUCAN-4-GLUCANOHYDROLASE, ALPHA-AMYLASE GLYCOSYLTRANSFERASE, GLYCOSYLTRANSFERASE; GLYCOSYLTRANSFERASE
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_guinier25.19 Å
Radius of gyration Rg (electron density) rg_electron24.13 Å
Forward intensity I(0) i048330800.00
Molecular weight molecular_weight53525.0 kDa
Excluded volume excluded_volume66501 ų
Envelope volume envelope_volume75675 ų
Hydration-shell volume shell_volume26911 ų
Envelope diameter envelope_diameter87.6 Å
Shell Rg shell_rg30.94 Å
Envelope Rg envelope_rg24.21 Å
Shape Rg shape_rg24.12 Å
Total Rg total_rg24.89 Å
Total atoms total_atoms3800
Residues n_residues469
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 dmax84.8 Å
Rg (real space) rg_real25.23 Å
Rg uncertainty (real space) rg_real_error0.61 Å
I(0) (real space) i0_real4.8330e+07
I(0) uncertainty (real space) i0_real_error7.2670e+05
Rg (reciprocal space) rg_reciprocal25.22 Å
I(0) (reciprocal space) i0_reciprocal48330000.0000
Solution quality estimate total_estimate0.8743
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.6 Å
Skewness Skewness skewness0.448
Kurtosis Kurtosis kurtosis-0.149
Angular range angular_range— – 0.3150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7266000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.812; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.954; Smooth: 0.974
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1bpl.1
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
Domain ID domain_idd1bplb1
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

CATH v4.4 (3 domains)

Domain ID domain_id1bplA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology750 — Transcription Regulator spoIIAA
Homologous superfamily homologous superfamily90 —
Domain ID domain_id1bplA02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily140 —
Domain ID domain_id1bplB02
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)