SAXSdb — 1vb9

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

alpha-amylase II

Thermoactinomyces vulgaris

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 1–585	Mutation：D325N	;alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-[alpha-D-glucopyranose-(1-6)]alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose ; × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；PEG6000, calcium chloride, Tris, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.233
2	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–585	Mutation：D325N	;alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-[alpha-D-glucopyranose-(1-6)]alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose ; × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；PEG6000, calcium chloride, Tris, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.233

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 1VB9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BVZ ALPHA-AMYLASE II (TVAII) FROM THERMOACTINOMYCES VULGARIS R-47 Deposited 1998-09-22	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 1–585（585 aa） Fragment：N,A,B.C	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.1；pH 6.1	Resolution 2.60 Å R-free 0.272
1BVZ ALPHA-AMYLASE II (TVAII) FROM THERMOACTINOMYCES VULGARIS R-47 Deposited 1998-09-22	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 1–585（585 aa） Fragment：N,A,B.C	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.1；pH 6.1	Resolution 2.60 Å R-free 0.272
1G1Y CRYSTAL STRUCTURE OF ALPHA-AMYLASE II (TVAII) FROM THERMOACTINOMYCES VULGARIS R-47 AND BETA-CYCLODEXTRIN COMPLEX Deposited 2000-10-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–585（585 aa） Chain B 1–585（585 aa）	Mutation：E354A Mutation：E354A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；284 K；MES, PEG6000, Calcium chloride, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 3.00 Å R-free 0.260
1JF5 CRYSTAL STRUCTURE OF THERMOACTINOMYCES VULGARIS R-47 ALPHA-AMYLASE 2 MUTANT F286A Deposited 2001-06-20	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 1–585（585 aa） Chain B 1–585（585 aa）	Mutation：F286A Mutation：F286A	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；298 K；PEG6000, MES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.20 Å R-free 0.273
1JF6 Crystal structure of thermoactinomyces vulgaris r-47 alpha-amylase mutant F286Y Deposited 2001-06-20	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 1–585（585 aa） Chain B 1–585（585 aa）	Mutation：F286Y Mutation：F286Y	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；298 K；PEG600, MES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.20 Å R-free 0.282
1JI2 Improved X-ray Structure of Thermoactinomyces vulgaris R-47 alpha-Amylase 2 Deposited 2001-06-28	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 1–585（585 aa） Chain B 1–585（585 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；298 K；PEG6000, MES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.30 Å R-free 0.224
1JIB Complex of Alpha-amylase II (TVA II) from Thermoactinomyces vulgaris R-47 with Maltotetraose Based on a Crystal Soaked with Maltohexaose. Deposited 2001-07-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–585（585 aa）	Mutation：D325N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；292 K；PEG6000, MES, CaCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 3.30 Å R-free 0.304
1JIB Complex of Alpha-amylase II (TVA II) from Thermoactinomyces vulgaris R-47 with Maltotetraose Based on a Crystal Soaked with Maltohexaose. Deposited 2001-07-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–585（585 aa）	Mutation：D325N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；292 K；PEG6000, MES, CaCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 3.30 Å R-free 0.304
1JL8 Complex of alpha-amylase II (TVA II) from Thermoactinomyces vulgaris R-47 with beta-cyclodextrin based on a co-crystallization with methyl beta-cyclodextrin Deposited 2001-07-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–585（585 aa）	Mutation：D325N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；292 K；MES, methyl beta-cyclodextrin, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 3.20 Å R-free 0.255
1JL8 Complex of alpha-amylase II (TVA II) from Thermoactinomyces vulgaris R-47 with beta-cyclodextrin based on a co-crystallization with methyl beta-cyclodextrin Deposited 2001-07-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–585（585 aa）	Mutation：D325N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；292 K；MES, methyl beta-cyclodextrin, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 3.20 Å R-free 0.255
1VFM Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase 2/alpha-cyclodextrin complex Deposited 2004-04-16	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–585（585 aa）	Mutation：D325N/D421N	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；298 K；PEG20000, calcium chloride, MES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.90 Å R-free 0.248
1VFM Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase 2/alpha-cyclodextrin complex Deposited 2004-04-16	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–585（585 aa）	Mutation：D325N/D421N	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；298 K；PEG20000, calcium chloride, MES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.90 Å R-free 0.248
1VFO Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase 2/beta-cyclodextrin complex Deposited 2004-04-16	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–585（585 aa）	Mutation：D325N/D421N	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；298 K；PEG20000, calcium chloride, MES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.81 Å R-free 0.256
1VFO Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase 2/beta-cyclodextrin complex Deposited 2004-04-16	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–585（585 aa）	Mutation：D325N/D421N	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；298 K；PEG20000, calcium chloride, MES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.81 Å R-free 0.256
1VFU Crystal structure of Thermoactinomyces vulgaris R-47 amylase 2/gamma-cyclodextrin complex Deposited 2004-04-19	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–585（585 aa）	Mutation：D325N/D421N	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；298 K；PEG20000, calcium chloride, MES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.10 Å R-free 0.284
1VFU Crystal structure of Thermoactinomyces vulgaris R-47 amylase 2/gamma-cyclodextrin complex Deposited 2004-04-19	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–585（585 aa）	Mutation：D325N/D421N	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；298 K；PEG20000, calcium chloride, MES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.10 Å R-free 0.284
1WZK Thermoactinomyces vulgaris R-47 alpha-amylase II (TVA II) mutatnt D465N Deposited 2005-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–585（585 aa） Chain B 1–585（585 aa）	Mutation：D465N Mutation：D465N	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；PEG6000, calcium chloride, Tris, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.248
1WZL Thermoactinomyces vulgaris R-47 alpha-amylase II (TVA II) mutatnt R469L Deposited 2005-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–585（585 aa） Chain B 1–585（585 aa）	Mutation：R469L Mutation：R469L	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；PEG6000, calcium chloride, Tris, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.229
1WZM Thermoactinomyces vulgaris R-47 alpha-amylase II (TVA II) mutatnt R469K Deposited 2005-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–585（585 aa） Chain B 1–585（585 aa）	Mutation：R469K Mutation：R469K	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；PEG6000, calcium chloride, Tris, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.20 Å R-free 0.293
2D2O Structure of a complex of Thermoactinomyces vulgaris R-47 alpha-amylase 2 with maltohexaose demonstrates the important role of aromatic residues at the reducing end of the substrate binding cleft Deposited 2005-09-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–585（585 aa） Chain B 1–585（585 aa）	Mutation：D325N Mutation：D325N	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；298 K；1.0 % (w/v) polyethylene glycol 6,000, 2.5mM calcium chloride, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.217
3A6O Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase 2/acarbose complex Deposited 2009-09-07	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 1–585（585 aa）	Not recorded	CA CALCIUM ION × 1 ARE ACARBOSE DERIVED PENTASACCHARIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	Resolution 2.80 Å R-free 0.231
3A6O Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase 2/acarbose complex Deposited 2009-09-07	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 1–585（585 aa）	Not recorded	CA CALCIUM ION × 1 ARE ACARBOSE DERIVED PENTASACCHARIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	Resolution 2.80 Å R-free 0.231

15 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NEPU2_THEVU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–585； UniProt 1–585 Author chain B； PDBConstruct 1–585； UniProt 1–585

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	1vb9
Deposition date deposition_date	2004-02-25
Structure title title	Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVA II) complexed with transglycosylated product
Keywords keywords	(beta/alpha)8 barrel, GH family 13, hydrolase; HYDROLASE
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	33.49 Å
Radius of gyration Rg (electron density) rg_electron	32.64 Å
Forward intensity I(0) i0	286179000.00
Molecular weight molecular_weight	136980.0 kDa
Excluded volume excluded_volume	171320 Å³
Envelope volume envelope_volume	204050 Å³
Hydration-shell volume shell_volume	50806 Å³
Envelope diameter envelope_diameter	113.7 Å
Shell Rg shell_rg	40.74 Å
Envelope Rg envelope_rg	32.64 Å
Shape Rg shape_rg	32.61 Å
Total Rg total_rg	33.32 Å
Total atoms total_atoms	9688
Residues n_residues	1170
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	106.4 Å
Rg (real space) rg_real	33.42 Å
Rg uncertainty (real space) rg_real_error	0.71 Å
I(0) (real space) i0_real	2.8620e+08
I(0) uncertainty (real space) i0_real_error	4.3270e+06
Rg (reciprocal space) rg_reciprocal	33.47 Å
I(0) (reciprocal space) i0_reciprocal	286200000.0000
Solution quality estimate total_estimate	0.8995
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	38.5 Å
Skewness Skewness skewness	0.271
Kurtosis Kurtosis kurtosis	-0.459
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	86790000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.941

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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	alpha-amylase II
Molecular weight formula_weight	67553.1 kDa
EC 编号 ec_number	3.2.1.1
Mutation mutation	D325N
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	10196

MLLEAIFHEAKGSYAYPISETQLRVRLRAKKGDVVRCEVLYADRYASPEEELAHALAGKAGSDERFDYFEALLECSTKRVKYVFLLTGPQGEAVYFGETGFSAERSKAGVFQYAYIHRSEVFTTPEWAKEAVIYQIFPERFANGDPSNDPPGTEQWAKDARPRHDSFYGGDLKGVIDRLPYLEELGVTALYFTPIFASPSHHKYDTADYLAIDPQFGDLPTFRRLVDEAHRRGIKIILDAVFNHAGDQFFAFRDVLQKGEQSRYKDWFFIEDFPVSKTSRTNYETFAVQVPAMPKLRTENPEVKEYLFDVARFWMEQGIDGWRLNVANEVDHAFWREFRRLVKSLNPDALIVGEIWHDASGWLMGDQFDSVMNYLFRESVIRFFATGEIHAERFDAELTRARMLYPEQAAQGLWNLLDSHDTERFLTSCGGNEAKFRLAVLFQMTYLGTPLIYYGDEIGMAGATDPDCRRPMIWEEKEQNRGLFEFYKELIRLRHRLASLTRGNVRSWHADKQANLYAFVRTVQDQHVGVVLNNRGEKQTVLLQVPESGGKTWLDCLTGEEVHGKQGQLKLTLRPYQGMILWNGR

来源 Source

来源生物 organism	Thermoactinomyces vulgaris
NCBI Class编号 ncbi_taxonomy_id	2026
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 branched

Description description	;alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-[alpha-D-glucopyranose-(1-6)]alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose ;
Molecular weight formula_weight	990.9 kDa
Source method src_method	man
Copy count entity_count	2

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	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	508

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7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1vb9a1
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	d1vb9a2
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	d1vb9a3
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	d1vb9b1
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	d1vb9b2
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	d1vb9b3
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	1vb9A01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1vb9A02
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	1vb9A03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	400 — Oligo-1,6-glucosidase; domain 2
Homologous superfamily homologous superfamily	10 — Oligo-1,6-glucosidase; Domain 2

Domain ID domain_id	1vb9A04
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	1vb9B01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1vb9B02
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	1vb9B03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	400 — Oligo-1,6-glucosidase; domain 2
Homologous superfamily homologous superfamily	10 — Oligo-1,6-glucosidase; Domain 2

Domain ID domain_id	1vb9B04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

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8. Citations (1)

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Unit-cell length a length_a	113.049 Å
Unit-cell length b length_b	118.274 Å
Unit-cell length c length_c	112.107 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	8

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

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	33.990 Å
R factor r_factor	0.1940
R_work r_work	0.1940
R_free r_free	0.2330

fit	/app/data/saxs_computation/vb/1vb9/1vb9.fit
pddf	/app/data/pr_computation/vb/1vb9/1vb9.pr.out
profile	/app/data/saxs_computation/vb/1vb9/1vb9.dat

Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVA II) complexed with transglycosylated product

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

alpha-amylase II

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