1ded

CRYSTAL STRUCTURE OF ALKALOPHILIC ASPARAGINE 233-REPLACED CYCLODEXTRIN GLUCANOTRANSFERASE COMPLEXED WITH AN INHIBITOR, ACARBOSE, AT 2.0 A RESOLUTION

Method: X-RAY DIFFRACTION D_max: 123.2 Å Quality: REASONABLE

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

CYCLODEXTRIN GLUCANOTRANSFERASE

Bacillus sp.

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 Homooligomer Protein × 2 其他Polymer 3 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 28–713 Chain B； UniProt 28–713	Fragment：CYCLODEXTRIN GLUCANOTRANSFERASE (CGTASE) Mutation：H233N	;4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose ; × 3 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；PEG 3000, ISO-PROPANOL, SODIUM CITRATE, ACARBOSE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.222

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 1DED	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D7F CRYSTAL STRUCTURE OF ASPARAGINE 233-REPLACED CYCLODEXTRIN GLUCANOTRANSFERASE FROM ALKALOPHILIC BACILLUS SP. 1011 DETERMINED AT 1.9 A RESOLUTION Deposited 1999-10-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 28–713（686 aa） Chain B 28–713（686 aa）	Mutation：H233N Mutation：H233N	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；SODIUM CITRATE, PEG 3000, ISO-PROPANOL, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.90 Å R-free 0.203
1I75 CRYSTAL STRUCTURE OF CYCLODEXTRIN GLUCANOTRANSFERASE FROM ALKALOPHILIC BACILLUS SP.#1011 COMPLEXED WITH 1-DEOXYNOJIRIMYCIN Deposited 2001-03-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 28–713（686 aa） Chain B 28–713（686 aa）	Not recorded	CA CALCIUM ION × 4 NOJ 1-DEOXYNOJIRIMYCIN × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；PEG3000, 2-Propanol, sodium citrate, calcium chloride, 1-deoxynojirimycin, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.214
1PAM CYCLODEXTRIN GLUCANOTRANSFERASE Deposited 1996-07-08	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 28–713（686 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；1% PROTEIN, 20% PEG3000, 20% 2 PROPANOL,0.1M NA CITRATE, PH 5.6	Resolution 1.80 Å R-free 0.211
1PAM CYCLODEXTRIN GLUCANOTRANSFERASE Deposited 1996-07-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 28–713（686 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；1% PROTEIN, 20% PEG3000, 20% 2 PROPANOL,0.1M NA CITRATE, PH 5.6	Resolution 1.80 Å R-free 0.211
1UKQ Crystal structure of cyclodextrin glucanotransferase complexed with a pseudo-maltotetraose derived from acarbose Deposited 2003-09-01	Different construct 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 28–713（686 aa）	Not recorded	GLC alpha-D-glucopyranose × 1 ACI 6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；PEG 3000, sodium citrate, 2-propanol, calcium chloride, acarbose, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.00 Å R-free 0.246
1UKQ Crystal structure of cyclodextrin glucanotransferase complexed with a pseudo-maltotetraose derived from acarbose Deposited 2003-09-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 28–713（686 aa）	Not recorded	GLC alpha-D-glucopyranose × 1 ACI 6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；PEG 3000, sodium citrate, 2-propanol, calcium chloride, acarbose, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.00 Å R-free 0.246
1UKS Crystal structure of F183L/F259L mutant cyclodextrin glucanotransferase complexed with a pseudo-maltotetraose derived from acarbose Deposited 2003-09-01	Different construct 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 28–713（686 aa）	Mutation：F183L/F259L	GLC alpha-D-glucopyranose × 1 ACI 6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；PEG 3000, SODIUM CITRATE, 2-PROPANOL, CALCIUM CHLORIDE, ACARBOSE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 1.90 Å R-free 0.215
1UKS Crystal structure of F183L/F259L mutant cyclodextrin glucanotransferase complexed with a pseudo-maltotetraose derived from acarbose Deposited 2003-09-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 28–713（686 aa）	Mutation：F183L/F259L	GLC alpha-D-glucopyranose × 1 ACI 6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；PEG 3000, SODIUM CITRATE, 2-PROPANOL, CALCIUM CHLORIDE, ACARBOSE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 1.90 Å R-free 0.215
1UKT Crystal structure of Y100L mutant cyclodextrin glucanotransferase compexed with an acarbose Deposited 2003-09-01	Different construct 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 28–713（686 aa）	Mutation：Y100L	ACI 6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；PEG 3000, SODIUM CITRATE, 2-PROPANOL, CALCIUM CHLORIDE, ACARBOSE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.20 Å R-free 0.276
1UKT Crystal structure of Y100L mutant cyclodextrin glucanotransferase compexed with an acarbose Deposited 2003-09-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 28–713（686 aa）	Mutation：Y100L	ACI 6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；PEG 3000, SODIUM CITRATE, 2-PROPANOL, CALCIUM CHLORIDE, ACARBOSE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.20 Å R-free 0.276
1V3J Crystal structure of F283L mutant cyclodextrin glycosyltransferase Deposited 2003-11-03	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 28–713（686 aa）	Mutation：F283L	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；PEG3000, SODIUM CITRATE, 2-PROPANOL, CALCIUM CHLORIDE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.00 Å R-free 0.242
1V3J Crystal structure of F283L mutant cyclodextrin glycosyltransferase Deposited 2003-11-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 28–713（686 aa）	Mutation：F283L	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；PEG3000, SODIUM CITRATE, 2-PROPANOL, CALCIUM CHLORIDE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.00 Å R-free 0.242
1V3K Crystal structure of F283Y mutant cyclodextrin glycosyltransferase Deposited 2003-11-03	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 28–713（686 aa）	Mutation：F283Y	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；PEG3000, SODIUM CITRATE, 2-PROPANOL, CALCIUM CHLORIDE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.00 Å R-free 0.200
1V3K Crystal structure of F283Y mutant cyclodextrin glycosyltransferase Deposited 2003-11-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 28–713（686 aa）	Mutation：F283Y	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；PEG3000, SODIUM CITRATE, 2-PROPANOL, CALCIUM CHLORIDE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.00 Å R-free 0.200
1V3L Crystal structure of F283L mutant cyclodextrin glycosyltransferase complexed with a pseudo-tetraose derived from acarbose Deposited 2003-11-03	Different construct 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 28–713（686 aa）	Mutation：F283L	GLC alpha-D-glucopyranose × 1 ACI 6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；PEG3000, SODIUM CITRATE, 2-PROPANOL, CALCIUM CHLORIDE, ACARBOSE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.10 Å R-free 0.232
1V3L Crystal structure of F283L mutant cyclodextrin glycosyltransferase complexed with a pseudo-tetraose derived from acarbose Deposited 2003-11-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 28–713（686 aa）	Mutation：F283L	GLC alpha-D-glucopyranose × 1 ACI 6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；PEG3000, SODIUM CITRATE, 2-PROPANOL, CALCIUM CHLORIDE, ACARBOSE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.10 Å R-free 0.232
1V3M Crystal structure of F283Y mutant cyclodextrin glycosyltransferase complexed with a pseudo-tetraose derived from acarbose Deposited 2003-11-03	Different construct 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 28–713（686 aa）	Mutation：F283Y	GLC alpha-D-glucopyranose × 3 ACI 6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL × 1 GAL beta-D-galactopyranose × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；PEG3000, SODIUM CITRATE, 2-PROPANOL, CALCIUM CHLORIDE, ACARBOSE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.00 Å R-free 0.218
1V3M Crystal structure of F283Y mutant cyclodextrin glycosyltransferase complexed with a pseudo-tetraose derived from acarbose Deposited 2003-11-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 28–713（686 aa）	Mutation：F283Y	GLC alpha-D-glucopyranose × 1 ACI 6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL × 1 GAL beta-D-galactopyranose × 2 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；PEG3000, SODIUM CITRATE, 2-PROPANOL, CALCIUM CHLORIDE, ACARBOSE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.00 Å R-free 0.218

10 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CDGT_BACS0
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–686； UniProt 28–713 Author chain B； PDBConstruct 1–686； UniProt 28–713

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	1ded
Deposition date deposition_date	1999-11-14
Structure title title	CRYSTAL STRUCTURE OF ALKALOPHILIC ASPARAGINE 233-REPLACED CYCLODEXTRIN GLUCANOTRANSFERASE COMPLEXED WITH AN INHIBITOR, ACARBOSE, AT 2.0 A RESOLUTION
Keywords keywords	CYCLODEXTRIN GLUCANOTRANSFERASE, CGTASE, ACARBOSE, 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	36.50 Å
Radius of gyration Rg (electron density) rg_electron	35.88 Å
Forward intensity I(0) i0	363845000.00
Molecular weight molecular_weight	152370.0 kDa
Excluded volume excluded_volume	189160 Å³
Envelope volume envelope_volume	229890 Å³
Hydration-shell volume shell_volume	53906 Å³
Envelope diameter envelope_diameter	124.7 Å
Shell Rg shell_rg	42.14 Å
Envelope Rg envelope_rg	35.35 Å
Shape Rg shape_rg	35.89 Å
Total Rg total_rg	36.24 Å
Total atoms total_atoms	13275
Residues n_residues	1372
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	123.2 Å
Rg (real space) rg_real	37.82 Å
Rg uncertainty (real space) rg_real_error	0.50 Å
I(0) (real space) i0_real	3.6270e+08
I(0) uncertainty (real space) i0_real_error	5.3580e+06
Rg (reciprocal space) rg_reciprocal	36.52 Å
I(0) (reciprocal space) i0_reciprocal	363800000.0000
Solution quality estimate total_estimate	0.6879
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	40.1 Å
Skewness Skewness skewness	0.483
Kurtosis Kurtosis kurtosis	-0.223
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	2.4210
Highest regularization parameter α highest_alpha	70740000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.871; Stabil: 0.898; Sysdev: 0.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.709

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	CYCLODEXTRIN GLUCANOTRANSFERASE
Molecular weight formula_weight	75206.0 kDa
EC 编号 ec_number	2.4.1.19
Mutation mutation	H233N
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	15555

APDTSVSNKQNFSTDVIYQIFTDRFSDGNPANNPTGAAFDGSCTNLRLYCGGDWQGIINKINDGYLTGMGITAIWISQPVENIYSVINYSGVNNTAYHGYWARDFKKTNPAYGTMQDFKNLIDTAHAHNIKVIIDFAPNHTSPASSDDPSFAENGRLYDNGNLLGGYTNDTQNLFHHYGGTDFSTIENGIYKNLYDLADLNHNNSSVDVYLKDAIKMWLDLGVDGIRVDAVKNMPFGWQKSFMATINNYKPVFTFGEWFLGVNEISPEYHQFANESGMSLLDFRFAQKARQVFRDNTDNMYGLKAMLEGSEVDYAQVNDQVTFIDNHDMERFHTSNGDRRKLEQALAFTLTSRGVPAIYYGSEQYMSGGNDPDNRARLPSFSTTTTAYQVIQKLAPLRKSNPAIAYGSTHERWINNDVIIYERKFGNNVAVVAINRNMNTPASITGLVTSLPRGSYNDVLGGILNGNTLTVGAGGAASNFTLAPGGTAVWQYTTDATTPIIGNVGPMMAKPGVTITIDGRGFGSGKGTVYFGTTAVTGADIVAWEDTQIQVKIPAVPGGIYDIRVANAAGAASNIYDNFEVLTGDQVTVRFVINNATTALGQNVFLTGNVSELGNWDPNNAIGPMYNQVVYQYPTWYYDVSVPAGQTIEFKFLKKQGSTVTWEGGANRTFTTPTSGTATVNVNWQP

来源 Source

来源生物 organism	Bacillus sp.
NCBI Class编号 ncbi_taxonomy_id	1410
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 branched

Description description	;4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose ;
Molecular weight formula_weight	645.6 kDa
Source method src_method	man
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	759

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1deda1
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	d1deda2
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	d1deda3
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	d1deda4
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

Domain ID domain_id	d1dedb1
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	d1dedb2
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	d1dedb3
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	d1dedb4
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 (8 domains)

Domain ID domain_id	1dedA01
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	1dedA02
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	1dedA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1dedA04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1dedB01
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	1dedB02
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	1dedB03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1dedB04
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 (1)

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Unit-cell length a length_a	64.930 Å
Unit-cell length b length_b	73.830 Å
Unit-cell length c length_c	79.050 Å
Unit-cell angle α angle_alpha	85.10 °
Unit-cell angle β angle_beta	105.40 °
Unit-cell angle γ angle_gamma	100.50 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1630
R_work r_work	0.1630
R_free r_free	0.2220

fit	/app/data/saxs_computation/de/1ded/1ded.fit
pddf	/app/data/pr_computation/de/1ded/1ded.pr.out
profile	/app/data/saxs_computation/de/1ded/1ded.dat