SAXSdb — 7cgt

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1. Protein Identity and Related Structures Protein Identity & Related Structures

CYCLODEXTRIN GLYCOSYLTRANSFERASE

Bacillus circulans

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 35–718	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

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 7CGT	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 mutation/modification Different experimental conditions 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
1CGU CATALYTIC CENTER OF CYCLODEXTRIN GLYCOSYLTRANSFERASE DERIVED FROM X-RAY STRUCTURE ANALYSIS COMBINED WITH SITE-DIRECTED MUTAGENESIS Deposited 1992-06-10	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination 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 2.50 Å
3CGT STRUCTURE OF CYCLODEXTRIN GLYCOSYLTRANSFERASE COMPLEXED WITH ITS MAIN PRODUCT BETA-CYCLODEXTRIN Deposited 1998-01-22	Different mutation/modification Different oligomeric state 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 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 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
8CGT STRUCTURE OF CYCLODEXTRIN GLYCOSYLTRANSFERASE COMPLEXED WITH A THIO-MALTOHEXAOSE Deposited 1998-09-27	Different mutation/modification Different oligomeric state 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 oligomeric state 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	CDGT1_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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7cgt
Deposition date deposition_date	1998-06-06
Structure title title	RAMEB COMPLEX OF CYCLODEXTRIN GLYCOSYLTRANSFERASE MUTANT
Keywords keywords	GLYCOSYLTRANSFERASE, STARCH DEGRADATION, CYCLODEXTRIN; GLYCOSYLTRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	26.58 Å
Radius of gyration Rg (electron density) rg_electron	25.44 Å
Forward intensity I(0) i0	92584700.00
Molecular weight molecular_weight	74536.0 kDa
Excluded volume excluded_volume	92585 Å³
Envelope volume envelope_volume	105170 Å³
Hydration-shell volume shell_volume	33820 Å³
Envelope diameter envelope_diameter	83.2 Å
Shell Rg shell_rg	33.48 Å
Envelope Rg envelope_rg	25.46 Å
Shape Rg shape_rg	25.42 Å
Total Rg total_rg	26.27 Å
Total atoms total_atoms	5266
Residues n_residues	684
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	80.4 Å
Rg (real space) rg_real	26.44 Å
Rg uncertainty (real space) rg_real_error	0.39 Å
I(0) (real space) i0_real	9.2580e+07
I(0) uncertainty (real space) i0_real_error	1.2060e+06
Rg (reciprocal space) rg_reciprocal	26.49 Å
I(0) (reciprocal space) i0_reciprocal	92590000.0000
Solution quality estimate total_estimate	0.9093
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.1 Å
Skewness Skewness skewness	0.161
Kurtosis Kurtosis kurtosis	-0.531
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15200000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.960; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.943

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	CYCLODEXTRIN GLYCOSYLTRANSFERASE
Molecular weight formula_weight	74521.0 kDa
EC 编号 ec_number	2.4.1.19
Mutation mutation	D229A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	5365

DPDTAVTNKQSFSTDVIYQVFTDRFLDGNPSNNPTGAAYDATCSNLKLYCGGDWQGLINKINDNYFSDLGVTALWISQPVENIFATINYSGVTNTAYHGYWARDFKKTNPYFGTMADFQNLITTAHAKGIKIVIDFAPNHTSPAMETDTSFAENGRLYDNGTLVGGYTNDTNGYFHHNGGSDFSSLENGIYKNLYDLADFNHNNATIDKYFKDAIKLWLDMGVDGIRVAAVKHMPLGWQKSWMSSIYAHKPVFTFGEWFLGSAASDADNTDFANKSGMSLLDFRFNSAVRNVFRDNTSNMYALDSMINSTATDYNQVNDQVTFIDNHDMDRFKTSAVNNRRLEQALAFTLTSRGVPAIYYGTEQYLTGNGDPDNRAKMPSFSKSTTAFNVISKLAPLRKSNPAIAYGSTQQRWINNDVYVYERKFGKSVAVVAVNRNLSTSASITGLSTSLPTGSYTDVLGGVLNGNNITSTNGSINNFTLAAGATAVWQYTTAETTPTIGHVGPVMGKPGNVVTIDGRGFGSTKGTVYFGTTAVTGAAITSWEDTQIKVTIPSVAAGNYAVKVAASGVNSNAYNNFTILTGDQVTVRFVVNNASTTLGQNLYLTGNVAELGNWSTGSTAIGPAFNQVIHQYPTWYYDVSVPAGKQLEFKFFKKNGSTITWESGSNHTFTTPASGTATVTVNWQ

来源 Source

来源生物 organism	Bacillus circulans
NCBI Class编号 ncbi_taxonomy_id	1397
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	99

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d7cgta1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.18 — E set domains
Family Family family	b.1.18.2 — E-set domains of sugar-utilizing enzymes

Domain ID domain_id	d7cgta2
Class class	b — All beta proteins
Fold Fold fold	b.3 — Prealbumin-like
Superfamily Superfamily superfamily	b.3.1 — Starch-binding domain-like
Family Family family	b.3.1.1 — Starch-binding domain

Domain ID domain_id	d7cgta3
Class class	b — All beta proteins
Fold Fold fold	b.71 — Glycosyl hydrolase domain
Superfamily Superfamily superfamily	b.71.1 — Glycosyl hydrolase domain
Family Family family	b.71.1.1 — alpha-Amylases, C-terminal beta-sheet domain

Domain ID domain_id	d7cgta4
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.8 — (Trans)glycosidases
Family Family family	c.1.8.1 — Amylase, catalytic domain

CATH v4.4 (4 domains)

Domain ID domain_id	7cgtA01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	80 — Glycosidases

Domain ID domain_id	7cgtA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

Domain ID domain_id	7cgtA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7cgtA04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (5)

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Unit-cell length a length_a	95.000 Å
Unit-cell length b length_b	104.800 Å
Unit-cell length c length_c	113.600 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1650
R_work r_work	0.1650
R_free r_free	0.2570

fit	/app/data/saxs_computation/cg/7cgt/7cgt.fit
pddf	/app/data/pr_computation/cg/7cgt/7cgt.pr.out
profile	/app/data/saxs_computation/cg/7cgt/7cgt.dat

RAMEB COMPLEX OF CYCLODEXTRIN GLYCOSYLTRANSFERASE MUTANT

1. Protein Identity and Related Structures Protein Identity & Related Structures

CYCLODEXTRIN GLYCOSYLTRANSFERASE

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction