SAXSdb — 1jd9

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

ALPHA-AMYLASE

Pseudoalteromonas haloplanktis

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 25–477	Mutation：K300Q	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；MPD, Hepes, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.50 Å R-free 0.245

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 1JD9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AQH ALPHA-AMYLASE FROM ALTEROMONAS HALOPLANCTIS Deposited 1997-07-30	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–477（453 aa）	Not recorded	CA CALCIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 2.00 Å R-free 0.204
1AQM ALPHA-AMYLASE FROM ALTEROMONAS HALOPLANCTIS COMPLEXED WITH TRIS Deposited 1997-07-31	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–477（453 aa）	Not recorded	CA CALCIUM ION × 1 CL CHLORIDE ION × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 1.85 Å R-free 0.186
1B0I ALPHA-AMYLASE FROM ALTEROMONAS HALOPLANCTIS Deposited 1998-11-10	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–477（453 aa）	Not recorded	CA CALCIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 2.40 Å R-free 0.217
1G94 CRYSTAL STRUCTURE ANALYSIS OF THE TERNARY COMPLEX BETWEEN PSYCHROPHILIC ALPHA AMYLASE FROM PSEUDOALTEROMONAS HALOPLANCTIS IN COMPLEX WITH A HEPTA-SACCHARIDE AND A TRIS MOLECULE Deposited 2000-11-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–472（448 aa）	Not recorded	CA CALCIUM ION × 1 CL CHLORIDE 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；292 K；MPD, Hepes, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.74 Å R-free 0.187
1G9H TERNARY COMPLEX BETWEEN PSYCHROPHILIC ALPHA-AMYLASE, COMII (PSEUDO TRI-SACCHARIDE FROM BAYER) AND TRIS (2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL) Deposited 2000-11-23	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 25–472（448 aa）	Not recorded	CA CALCIUM ION × 1 CL CHLORIDE 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；293 K；MPD, Hepes, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.201
1JD7 CRYSTAL STRUCTURE ANALYSIS OF THE MUTANT K300R OF PSEUDOALTEROMONAS HALOPLANCTIS ALPHA-AMYLASE Deposited 2001-06-13	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–477（453 aa）	Mutation：K300R	CA CALCIUM ION × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；MPD, Hepes, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.25 Å R-free 0.215
1KXH Crystal structure of the complex between an inactive mutant of psychrophilic alpha-amylase (D174N) and acarbose Deposited 2002-01-31	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 25–472（448 aa）	Mutation：D174N	CA CALCIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；MPD, hepes, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.188
1L0P CRYSTAL STRUCTURE ANALYSIS OF THE COMPLEX BETWEEN PSYCHROPHILIC ALPHA AMYLASE FROM PSEUDOALTEROMONAS HALOPLANCTIS AND NITRATE Deposited 2002-02-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–472（448 aa）	Not recorded	CA CALCIUM ION × 1 NO3 NITRATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；MPD, Hepes, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.10 Å R-free 0.180
8CQF Crystal Structure of a Chimeric Alpha-Amylase from Pseudoalteromonas Haloplanktis Complexed with Rearranged Acarbose Deposited 2023-03-06	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 26–232（207 aa） Chain A 236–294（59 aa） Chain A 301–471（171 aa）	Mutation：A77V Q204L S226G T227A E228K N231T T232L G270_G271insA A272G G273S N274S V275I I276L D310N T311D D312W Mutation：A77V Q204L S226G T227A E228K N231T T232L G270_G271insA A272G G273S N274S V275I I276L D310N T311D D312W Mutation：A77V Q204L S226G T227A E228K N231T T232L G270_G271insA A272G G273S N274S V275I I276L D310N T311D D312W	CL CHLORIDE ION × 2 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；3 M NaCl, 0.1 M BisTris	Resolution 2.05 Å R-free 0.198
8CQG Crystal Structure of a Chimeric Alpha-Amylase from Pseudoalteromonas Haloplanktis Deposited 2023-03-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–232（208 aa） Chain A 236–294（59 aa） Chain A 302–471（170 aa）	Mutation：A77V Q204L S226G T227A E228K N231T T232L G270_G271insA A272G G273S N274S V275I I276L D310N T311D D312W Mutation：A77V Q204L S226G T227A E228K N231T T232L G270_G271insA A272G G273S N274S V275I I276L D310N T311D D312W Mutation：A77V Q204L S226G T227A E228K N231T T232L G270_G271insA A272G G273S N274S V275I I276L D310N T311D D312W	EDO 1,2-ETHANEDIOL × 11 CL CHLORIDE ION × 2 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；3 M NaCl, 0.1 M BisTris	Resolution 1.74 Å R-free 0.205

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

View Construct and Data Evidence

UniProt name	AMY_ALTHA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–453； UniProt 25–477

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	1jd9
Deposition date deposition_date	2001-06-13
Structure title title	CRYSTAL STRUCTURE ANALYSIS OF THE MUTANT K300Q OF PSEUDOALTEROMONAS HALOPLANCTIS ALPHA-AMYLASE
Keywords keywords	ALPHA-BETA BARREL, GLYCOSYL HYDROLASE, ALLOSTERIC ACTIVATION, 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	23.62 Å
Radius of gyration Rg (electron density) rg_electron	22.48 Å
Forward intensity I(0) i0	43929000.00
Molecular weight molecular_weight	48853.0 kDa
Excluded volume excluded_volume	59844 Å³
Envelope volume envelope_volume	68256 Å³
Hydration-shell volume shell_volume	25531 Å³
Envelope diameter envelope_diameter	81.3 Å
Shell Rg shell_rg	29.40 Å
Envelope Rg envelope_rg	22.62 Å
Shape Rg shape_rg	22.44 Å
Total Rg total_rg	23.33 Å
Total atoms total_atoms	3444
Residues n_residues	448
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	79.2 Å
Rg (real space) rg_real	23.59 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	4.3930e+07
I(0) uncertainty (real space) i0_real_error	6.3570e+05
Rg (reciprocal space) rg_reciprocal	23.60 Å
I(0) (reciprocal space) i0_reciprocal	43930000.0000
Solution quality estimate total_estimate	0.8760
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.2 Å
Skewness Skewness skewness	0.365
Kurtosis Kurtosis kurtosis	-0.240
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7238000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.818; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.940

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	ALPHA-AMYLASE
Molecular weight formula_weight	49379.8 kDa
EC 编号 ec_number	3.2.1.1
Mutation mutation	K300Q
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	3634

TPTTFVHLFEWNWQDVAQECEQYLGPKGYAAVQVSPPNEHITGSQWWTRYQPVSYELQSRGGNRAQFIDMVNRCSAAGVDIYVDTLINHMAAGSGTGTAGNSFGNKSFPIYSPQDFHESCTINNSDYGNDRYRVQNCELVGLADLDTASNYVQNTIAAYINDLQAIGVKGFRFDASKHVAASDIQSLMAKVNGSPVVFQEVIDQGGEAVGASEYLSTGLVTEFKYSTELGNTFRNGSLAWLSNFGEGWGFMPSSSAVVFVDNHDNQRGHGGAGNVITFEDGRLYDLANVFMLAYPYGYPQVMSSYDFHGDTDAGGPNVPVHNNGNLECFASNWKCEHRWSYIAGGVDFRNNTADNWAVTNWWDNTNNQISFGRGSSGHMAINKEDSTLTATVQTDMASGQYCNVLKGELSADAKSCSGEVITVNSDGTINLNIGAWDAMAIHKNAKLNTSSAS

来源 Source

来源生物 organism	Pseudoalteromonas haloplanktis
NCBI Class编号 ncbi_taxonomy_id	228
宿主生物 host_organism	Escherichia coli

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	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	190

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1jd9a1
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	d1jd9a2
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 (2 domains)

Domain ID domain_id	1jd9A01
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	1jd9A02
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 (3)

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Unit-cell length a length_a	71.500 Å
Unit-cell length b length_b	138.400 Å
Unit-cell length c length_c	115.400 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	42.700 Å
R factor r_factor	—
R_work r_work	0.1800
R_free r_free	0.2450

fit	/app/data/saxs_computation/jd/1jd9/1jd9.fit
pddf	/app/data/pr_computation/jd/1jd9/1jd9.pr.out
profile	/app/data/saxs_computation/jd/1jd9/1jd9.dat

CRYSTAL STRUCTURE ANALYSIS OF THE MUTANT K300Q OF PSEUDOALTEROMONAS HALOPLANCTIS 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