3bmw

Cyclodextrin glycosyl transferase from Thermoanerobacterium thermosulfurigenes EM1 mutant S77P complexed with a maltoheptaose inhibitor

Method: X-RAY DIFFRACTION D_max: 79.3 Å Quality: EXCELLENT

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

Cyclomaltodextrin glucanotransferase

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	Mutation：S77P	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-(1-4)-alpha-D-glucopyranose × 1 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

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 3BMW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A47 CGTASE FROM THERMOANAEROBACTERIUM THERMOSULFURIGENES EM1 IN COMPLEX WITH A MALTOHEXAOSE INHIBITOR Deposited 1998-02-11	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）	Not recorded	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
1CIU THERMOSTABLE CGTASE FROM THERMOANAEROBACTERIUM THERMOSULFURIGENES EM1 AT PH 8.0. Deposited 1995-10-23	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）	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 oligomeric state Different ligand/ion 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

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3bmw
Deposition date deposition_date	2007-12-13
Structure title title	Cyclodextrin glycosyl transferase from Thermoanerobacterium thermosulfurigenes EM1 mutant S77P complexed with a maltoheptaose inhibitor
Keywords keywords	;glycosidase, thermostable, family 13 glycosyl hydrolas, ligand, substrate, acarbose, Glycosyltransferase, Metal-binding, Secreted, Transferase ;; TRANSFERASE
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	26.66 Å
Radius of gyration Rg (electron density) rg_electron	25.44 Å
Forward intensity I(0) i0	100928000.00
Molecular weight molecular_weight	77877.0 kDa
Excluded volume excluded_volume	96670 Å³
Envelope volume envelope_volume	109230 Å³
Hydration-shell volume shell_volume	34800 Å³
Envelope diameter envelope_diameter	82.2 Å
Shell Rg shell_rg	33.79 Å
Envelope Rg envelope_rg	25.61 Å
Shape Rg shape_rg	25.43 Å
Total Rg total_rg	26.28 Å
Total atoms total_atoms	5488
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	79.3 Å
Rg (real space) rg_real	26.51 Å
Rg uncertainty (real space) rg_real_error	0.48 Å
I(0) (real space) i0_real	1.0090e+08
I(0) uncertainty (real space) i0_real_error	1.4770e+06
Rg (reciprocal space) rg_reciprocal	26.56 Å
I(0) (reciprocal space) i0_reciprocal	100900000.0000
Solution quality estimate total_estimate	0.9120
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.4 Å
Skewness Skewness skewness	0.164
Kurtosis Kurtosis kurtosis	-0.539
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	21700000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.963; Stabil: 0.995; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.985

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Description description	Cyclomaltodextrin glucanotransferase
Molecular weight formula_weight	75508.1 kDa
EC 编号 ec_number	2.4.1.19
Mutation mutation	S77P
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	6689

ASDTAVSNVVNYSTDVIYQIVTDRFVDGNTSNNPTGDLYDPTHTSLKKYFGGDWQGIINKINDGYLTGMGVTAIWIPQPVENIYAVLPDSTFGGSTSYHGYWARDFKRTNPYFGSFTDFQNLINTAHAHNIKVIIDFAPNHTSPASETDPTYAENGRLYDNGTLLGGYTNDTNGYFHHYGGTDFSSYEDGIYRNLFDLADLNQQNSTIDSYLKSAIKVWLDMGIDGIRLDAVKHMPFGWQKNFMDSILSYRPVFTFGEWFLGTNEIDVNNTYFANESGMSLLDFRFSQKVRQVFRDNTDTMYGLDSMIQSTASDYNFINDMVTFIDNHDMDRFYNGGSTRPVEQALAFTLTSRGVPAIYYGTEQYMTGNGDPYNRAMMTSFNTSTTAYNVIKKLAPLRKSNPAIAYGTTQQRWINNDVYIYERKFGNNVALVAINRNLSTSYNITGLYTALPAGTYTDVLGGLLNGNSISVASDGSVTPFTLSAGEVAVWQYVSSSNSPLIGHVGPTMTKAGQTITIDGRGFGTTSGQVLFGSTAGTIVSWDDTEVKVKVPSVTPGKYNISLKTSSGATSNTYNNINILTGNQICVRFVVNNASTVYGENVYLTGNVAELGNWDTSKAIGPMFNQVVYQYPTWYYDVSVPAGTTIQFKFIKKNGNTITWEGGSNHTYTVPSSSTGTVIVNWQQ

来源 Source

来源生物 organism	Thermoanaerobacterium thermosulfurigenes
NCBI Class编号 ncbi_taxonomy_id	33950
宿主生物 host_organism	Bacillus subtilis

Entity 2 Entity 2 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 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-(1-4)-alpha-D-glucopyranose
Molecular weight formula_weight	504.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL
Molecular weight formula_weight	175.2 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 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 9 Entity 9 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1155

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3bmwa1
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	d3bmwa2
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	d3bmwa3
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	d3bmwa4
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	3bmwA01
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	3bmwA02
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	3bmwA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3bmwA04
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	73.791 Å
Unit-cell length b length_b	96.582 Å
Unit-cell length c length_c	115.241 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	1.600 Å
Low-resolution limit resolution_low	49.480 Å
R factor r_factor	0.1454
R_work r_work	0.1443
R_free r_free	0.1651

fit	/app/data/saxs_computation/bm/3bmw/3bmw.fit
pddf	/app/data/pr_computation/bm/3bmw/3bmw.pr.out
profile	/app/data/saxs_computation/bm/3bmw/3bmw.dat