SAXSdb — 1a47

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

CYCLODEXTRIN GLYCOSYLTRANSFERASE

Thermoanaerobacterium thermosulfurigenes

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 3 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 28–710	Not recorded	alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 alpha-D-quinovopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 ADH 1-AMINO-2,3-DIHYDROXY-5-HYDROXYMETHYL CYCLOHEX-5-ENE × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.7；21% SATURATED AMMONIUM SULFATE, 100 MM TRIS, PH 7.7	Resolution 2.56 Å R-free 0.250

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 1A47	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CIU THERMOSTABLE CGTASE FROM THERMOANAEROBACTERIUM THERMOSULFURIGENES EM1 AT PH 8.0. Deposited 1995-10-23	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 28–710（683 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å R-free 0.200
3BMV Cyclodextrin glycosyl transferase from Thermoanerobacterium thermosulfurigenes EM1 mutant S77P Deposited 2007-12-13	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 28–710（683 aa）	Mutation：S77P	CA CALCIUM ION × 2 SO4 SULFATE ION × 5 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；20% Ammonium sulfate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.163
3BMW Cyclodextrin glycosyl transferase from Thermoanerobacterium thermosulfurigenes EM1 mutant S77P complexed with a maltoheptaose inhibitor Deposited 2007-12-13	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–710（683 aa）	Mutation：S77P	ACI 6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL × 1 CA CALCIUM ION × 2 CL CHLORIDE ION × 1 SO4 SULFATE ION × 3 GOL GLYCEROL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；20% Ammonium sulfate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.165

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CDGT_THETU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–683； UniProt 28–710

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	1a47
Deposition date deposition_date	1998-02-11
Structure title title	CGTASE FROM THERMOANAEROBACTERIUM THERMOSULFURIGENES EM1 IN COMPLEX WITH A MALTOHEXAOSE INHIBITOR
Keywords keywords	GLYCOSIDASE, THERMOSTABLE, FAMILY 13 GLYCOSYL HYDROLASE, LIGAND, SUBSTRATE, ACARBOSE; GLYCOSIDASE
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	26.65 Å
Radius of gyration Rg (electron density) rg_electron	25.50 Å
Forward intensity I(0) i0	97476300.00
Molecular weight molecular_weight	76992.0 kDa
Excluded volume excluded_volume	95746 Å³
Envelope volume envelope_volume	108530 Å³
Hydration-shell volume shell_volume	34614 Å³
Envelope diameter envelope_diameter	83.3 Å
Shell Rg shell_rg	33.77 Å
Envelope Rg envelope_rg	25.62 Å
Shape Rg shape_rg	25.50 Å
Total Rg total_rg	26.30 Å
Total atoms total_atoms	5435
Residues n_residues	683
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	80.0 Å
Rg (real space) rg_real	26.50 Å
Rg uncertainty (real space) rg_real_error	0.45 Å
I(0) (real space) i0_real	9.7480e+07
I(0) uncertainty (real space) i0_real_error	1.2710e+06
Rg (reciprocal space) rg_reciprocal	26.55 Å
I(0) (reciprocal space) i0_reciprocal	97480000.0000
Solution quality estimate total_estimate	0.9125
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.3 Å
Skewness Skewness skewness	0.160
Kurtosis Kurtosis kurtosis	-0.542
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	19530000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.961; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.990

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	CYCLODEXTRIN GLYCOSYLTRANSFERASE
Molecular weight formula_weight	75498.1 kDa
EC 编号 ec_number	2.4.1.19
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	5620

ASDTAVSNVVNYSTDVIYQIVTDRFVDGNTSNNPTGDLYDPTHTSLKKYFGGDWQGIINKINDGYLTGMGVTAIWISQPVENIYAVLPDSTFGGSTSYHGYWARDFKRTNPYFGSFTDFQNLINTAHAHNIKVIIDFAPNHTSPASETDPTYAENGRLYDNGTLLGGYTNDTNGYFHHYGGTDFSSYEDGIYRNLFDLADLNQQNSTIDSYLKSAIKVWLDMGIDGIRLDAVKHMPFGWQKNFMDSILSYRPVFTFGEWFLGTNEIDVNNTYFANESGMSLLDFRFSQKVRQVFRDNTDTMYGLDSMIQSTASDYNFINDMVTFIDNHDMDRFYNGGSTRPVEQALAFTLTSRGVPAIYYGTEQYMTGNGDPYNRAMMTSFNTSTTAYNVIKKLAPLRKSNPAIAYGTTQQRWINNDVYIYERKFGNNVALVAINRNLSTSYNITGLYTALPAGTYTDVLGGLLNGNSISVASDGSVTPFTLSAGEVAVWQYVSSSNSPLIGHVGPTMTKAGQTITIDGRGFGTTSGQVLFGSTAGTIVSWDDTEVKVKVPSVTPGKYNISLKTSSGATSNTYNNINILTGNQICVRFVVNNASTVYGENVYLTGNVAELGNWDTSKAIGPMFNQVVYQYPTWYYDVSVPAGTTIQFKFIKKNGNTITWEGGSNHTYTVPSSSTGTVIVNWQQ

来源 Source

来源生物 organism	Thermoanaerobacterium thermosulfurigenes
NCBI Class编号 ncbi_taxonomy_id	33950
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 branched

Description description	alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
Molecular weight formula_weight	504.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 branched

Description description	alpha-D-quinovopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
Molecular weight formula_weight	488.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 branched

Description description	alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
Molecular weight formula_weight	342.3 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	1-AMINO-2,3-DIHYDROXY-5-HYDROXYMETHYL CYCLOHEX-5-ENE
Molecular weight formula_weight	159.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

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

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	185

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1a47a1
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	d1a47a2
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	d1a47a3
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	d1a47a4
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	1a47A01
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	1a47A02
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	1a47A03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1a47A04
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 (3)

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Unit-cell length a length_a	73.996 Å
Unit-cell length b length_b	97.789 Å
Unit-cell length c length_c	116.263 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	2.560 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1910
R_work r_work	0.1860
R_free r_free	0.2500

fit	/app/data/saxs_computation/a4/1a47/1a47.fit
pddf	/app/data/pr_computation/a4/1a47/1a47.pr.out
profile	/app/data/saxs_computation/a4/1a47/1a47.dat

CGTASE FROM THERMOANAEROBACTERIUM THERMOSULFURIGENES EM1 IN COMPLEX WITH A MALTOHEXAOSE INHIBITOR