SAXSdb — 3bh4

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

Alpha-amylase

Bacillus amyloliquefaciens

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 32–514	Not recorded	CA CALCIUM ION × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；100mM Tris-HCl, pH7.5, 24% PEG3350, 3.5mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.40 Å R-free 0.219
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 32–514	Not recorded	CA CALCIUM ION × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；100mM Tris-HCl, pH7.5, 24% PEG3350, 3.5mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.40 Å R-free 0.219

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 3BH4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1E3X Native structure of chimaeric amylase from B. amyloliquefaciens and B. licheniformis at 1.92A Deposited 2000-06-26	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 32–331（300 aa）	Not recorded	CA CALCIUM ION × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；CRYSTALS WERE GROWN AT 18C USING THE HANGING DROP METHOD WITH 8-13% MONOMETHYL ETHER POLYETHYLENE GLYCOL 2000 OR 5000 AS PRECIPITANT. DROPS WERE BUFFERED WITH 0.1M TRIS/HCL PH 7.5 CONTAINING 5MM CACL2 AND THE PROTEIN CONCENTRATION WAS 30-35MG/ML.	Resolution 1.90 Å R-free 0.200
1E3Z Acarbose complex of chimaeric amylase from B. amyloliquefaciens and B. licheniformis at 1.93A Deposited 2000-06-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 32–331（300 aa）	Not recorded	CA CALCIUM ION × 4 NA SODIUM ION × 1 ACI 6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；CRYSTALS WERE GROWN AT 18C USING THE HANGING DROP METHOD WITH 8-13% MONOMETHYL ETHER POLYETHYLENE GLYCOL 2000 OR 5000 AS PRECIPITANT. DROPS WERE BUFFERED WITH 0.1M TRIS/HCL PH 7.5 CONTAINING 5MM CACL2 AND THE PROTEIN CONCENTRATION WAS 30-35MG/ML. CRYSTALS WERE THEN SOAKED IN 10MM ACARBOSE SOLUTION TO OBTAIN THE COMPLEX.	Resolution 1.93 Å R-free 0.200
1E40 Tris/maltotriose complex of chimaeric amylase from B. amyloliquefaciens and B. licheniformis at 2.2A Deposited 2000-06-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 32–331（300 aa）	Not recorded	CA CALCIUM ION × 4 NA SODIUM ION × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；CRYSTALS WERE GROWN AT 18C USING THE HANGING DROP METHOD WITH 8-13% MONOMETHYL ETHER POLYETHYLENE GLYCOL 2000 OR 5000 AS PRECIPITANT. DROPS WERE BUFFERED WITH 0.1M TRIS/HCL PH 7.5 CONTAINING 5MM CACL2 AND THE PROTEIN CONCENTRATION WAS 30-35MG/ML. CRYSTALS WERE THEN SOAKED IN 10MM MALTOTRIOSE SOLUTION TO OBTAIN THE COMPLEX.	Resolution 2.20 Å R-free 0.210
1E43 Native structure of chimaeric amylase from B. amyloliquefaciens and B. licheniformis at 1.7A Deposited 2000-06-27	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 32–331（300 aa）	Not recorded	CA CALCIUM ION × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10；291 K；CRYSTALS WERE GROWN AT 18C USING THE HANGING DROP METHOD WITH 8-13% MONOMETHYL ETHER POLYETHYLENE GLYCOL 2000 OR 5000 AS PRECIPITANT. DROPS WERE BUFFERED WITH 0.1M TRIS/HCL PH 7.5 CONTAINING 5MM CACL2 AND THE PROTEIN CONCENTRATION WAS 30-35MG/ML.	Resolution 1.70 Å R-free 0.185

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AMY_BACAM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–483； UniProt 32–514 Author chain B； PDBConstruct 1–483； UniProt 32–514

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	3bh4
Deposition date deposition_date	2007-11-28
Structure title title	High resolution crystal structure of Bacillus amyloliquefaciens alpha-amylase
Keywords keywords	crystal structure alpha-amylase, Calcium, Carbohydrate metabolism, Glycosidase, Hydrolase, Metal-binding, Secreted; 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	34.83 Å
Radius of gyration Rg (electron density) rg_electron	34.24 Å
Forward intensity I(0) i0	192801000.00
Molecular weight molecular_weight	110010.0 kDa
Excluded volume excluded_volume	136420 Å³
Envelope volume envelope_volume	160540 Å³
Hydration-shell volume shell_volume	39865 Å³
Envelope diameter envelope_diameter	125.7 Å
Shell Rg shell_rg	39.61 Å
Envelope Rg envelope_rg	34.12 Å
Shape Rg shape_rg	34.23 Å
Total Rg total_rg	34.65 Å
Total atoms total_atoms	7788
Residues n_residues	966
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	119.4 Å
Rg (real space) rg_real	34.92 Å
Rg uncertainty (real space) rg_real_error	1.34 Å
I(0) (real space) i0_real	1.9280e+08
I(0) uncertainty (real space) i0_real_error	3.5240e+06
Rg (reciprocal space) rg_reciprocal	34.87 Å
I(0) (reciprocal space) i0_reciprocal	192800000.0000
Solution quality estimate total_estimate	0.8728
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	34.5 Å
Skewness Skewness skewness	0.393
Kurtosis Kurtosis kurtosis	-0.305
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	25050000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.846; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.952; Smooth: 0.853

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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
Molecular weight formula_weight	54902.2 kDa
EC 编号 ec_number	3.2.1.1
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	8435

VNGTLMQYFEWYTPNDGQHWKRLQNDAEHLSDIGITAVWIPPAYKGLSQSDNGYGPYDLYDLGEFQQKGTVRTKYGTKSELQDAIGSLHSRNVQVYGDVVLNHKAGADATEDVTAVEVNPANRNQETSEEYQIKAWTDFRFPGRGNTYSDFKWHWYHFDGADWDESRKISRIFKFRGEGKAWDWEVSSENGNYDYLMYADVDYDHPDVVAETKKWGIWYANELSLDGFRIDAAKHIKFSFLRDWVQAVRQATGKEMFTVAEYWQNNAGKLENYLNKTSFNQSVFDVPLHFNLQAASSQGGGYDMRRLLDGTVVSRHPEKAVTFVENHDTQPGQSLESTVQTWFKPLAYAFILTRESGYPQVFYGDMYGTKGTSPKEIPSLKDNIEPILKARKEYAYGPQHDYIDHPDVIGWTREGDSSAAKSGLAALITDGPGGSKRMYAGLKNAGETWYDITGNRSDTVKIGSDGWGEFHVNDGSVSIYVQK

来源 Source

来源生物 organism	Bacillus amyloliquefaciens
NCBI Class编号 ncbi_taxonomy_id	1390

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	8

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 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	647

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	3bh4A01
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	3bh4A02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	3bh4A03
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	3bh4B01
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	3bh4B02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	3bh4B03
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	89.760 Å
Unit-cell length b length_b	148.676 Å
Unit-cell length c length_c	76.197 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2060
R_work r_work	0.2060
R_free r_free	0.2190

fit	/app/data/saxs_computation/bh/3bh4/3bh4.fit
pddf	/app/data/pr_computation/bh/3bh4/3bh4.pr.out
profile	/app/data/saxs_computation/bh/3bh4/3bh4.dat

High resolution crystal structure of Bacillus amyloliquefaciens alpha-amylase

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

Alpha-amylase

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