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1cgu

CATALYTIC CENTER OF CYCLODEXTRIN GLYCOSYLTRANSFERASE DERIVED FROM X-RAY STRUCTURE ANALYSIS COMBINED WITH SITE-DIRECTED MUTAGENESIS

Method: X-RAY DIFFRACTION Dmax: 80.4 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

CYCLODEXTRIN GLYCOSYL-TRANSFERASE

Bacillus circulans

UniProt P30920

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 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 35–718 Not recorded alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.50 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 1CGU Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CGT STRUCTURE OF CYCLODEXTRIN GLYCOSYLTRANSFERASE REFINED AT 2.0 ANGSTROMS RESOLUTION Deposited 1992-06-10 Different oligomeric state Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 35–718（684 aa）
Not recorded CA CALCIUM ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
3CGT STRUCTURE OF CYCLODEXTRIN GLYCOSYLTRANSFERASE COMPLEXED WITH ITS MAIN PRODUCT BETA-CYCLODEXTRIN Deposited 1998-01-22 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 35–718（684 aa）
Mutation：E257A CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.9；pH 6.9
Resolution 2.40 Å R-free 0.228
4CGT DELETION MUTANT DELTA(145-150), F151D OF CYCLODEXTRIN GLYCOSYLTRANSFERASE Deposited 1998-06-06 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 35–718（684 aa）
Mutation：DEL(145-150), F151D CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.9；pH 6.9
Resolution 2.60 Å R-free 0.272
5CGT MALTOTRIOSE COMPLEX OF PRECONDITIONED CYCLODEXTRIN GLYCOSYLTRANSFERASE MUTANT Deposited 1998-06-06 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 35–718（684 aa）
Mutation：D229A GLC alpha-D-glucopyranose × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.9；pH 6.9
Resolution 2.50 Å R-free 0.247
6CGT HOXA COMPLEX OF CYCLODEXTRIN GLYCOSYLTRANSFERASE MUTANT Deposited 1998-06-06 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 35–718（684 aa）
Mutation：L194T OPG OXIRANPSEUDOGLUCOSE × 2 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.9；pH 6.9
Resolution 2.60 Å R-free 0.246
7CGT RAMEB COMPLEX OF CYCLODEXTRIN GLYCOSYLTRANSFERASE MUTANT Deposited 1998-06-06 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 35–718（684 aa）
Mutation：D229A CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.9；pH 6.9 THE SUBMITTED PDB FILE RESULTED FROM A SOAK OF CGTASE MUTANT D229A WITH A 1.8 TIMES RANDOMLY METHYLATED BETA-CYCLODEXTRIN (RAMEB). THE STRUCTURE WAS REFINED WITH A NON-METHYLATED BETA-CYCLODEXTRIN MODEL WHICH IS NOT INCLUDED IN THE PDB FILE BECAUSE OF INSUFFICIENT DENSITY.
Resolution 3.00 Å R-free 0.257
8CGT STRUCTURE OF CYCLODEXTRIN GLYCOSYLTRANSFERASE COMPLEXED WITH A THIO-MALTOHEXAOSE Deposited 1998-09-27 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 35–718（684 aa）
Mutation：E257A CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.9；pH 6.9
Resolution 2.40 Å R-free 0.178
9CGT STRUCTURE OF CYCLODEXTRIN GLYCOSYLTRANSFERASE COMPLEXED WITH A THIO-MALTOPENTAOSE Deposited 1998-09-27 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 35–718（684 aa）
Mutation：E257A CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.9；pH 6.9
Resolution 2.50 Å R-free 0.182

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CDGT_BACCI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–684； UniProt 35–718

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 1cgu

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1cgu
Deposition date deposition_date1992-06-10
Structure title titleCATALYTIC CENTER OF CYCLODEXTRIN GLYCOSYLTRANSFERASE DERIVED FROM X-RAY STRUCTURE ANALYSIS COMBINED WITH SITE-DIRECTED MUTAGENESIS
Keywords keywordsGLYCOSYLTRANSFERASE; 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_guinier26.60 Å
Radius of gyration Rg (electron density) rg_electron25.46 Å
Forward intensity I(0) i093143900.00
Molecular weight molecular_weight74862.0 kDa
Excluded volume excluded_volume92987 ų
Envelope volume envelope_volume105470 ų
Hydration-shell volume shell_volume33861 ų
Envelope diameter envelope_diameter83.0 Å
Shell Rg shell_rg33.55 Å
Envelope Rg envelope_rg25.53 Å
Shape Rg shape_rg25.44 Å
Total Rg total_rg26.29 Å
Total atoms total_atoms5288
Residues n_residues684
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 dmax80.4 Å
Rg (real space) rg_real26.46 Å
Rg uncertainty (real space) rg_real_error0.50 Å
I(0) (real space) i0_real9.3140e+07
I(0) uncertainty (real space) i0_real_error1.3200e+06
Rg (reciprocal space) rg_reciprocal26.50 Å
I(0) (reciprocal space) i0_reciprocal93150000.0000
Solution quality estimate total_estimate0.9121
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.2 Å
Skewness Skewness skewness0.166
Kurtosis Kurtosis kurtosis-0.526
Angular range angular_range— – 0.3000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha16140000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.958; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.989
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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) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1cgua1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.18 — E set domains
Family Family familyb.1.18.2 — E-set domains of sugar-utilizing enzymes
Domain ID domain_idd1cgua2
Class classb — All beta proteins
Fold Fold foldb.3 — Prealbumin-like
Superfamily Superfamily superfamilyb.3.1 — Starch-binding domain-like
Family Family familyb.3.1.1 — Starch-binding domain
Domain ID domain_idd1cgua3
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_idd1cgua4
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 (4 domains)

Domain ID domain_id1cguA01
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
Domain ID domain_id1cguA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1180 — Golgi alpha-mannosidase II
Domain ID domain_id1cguA03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1cguA04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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8. Citations (5)

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9. Files and Curves (10)