SAXSdb — 9xvp

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

Isoamylase 2, chloroplastic

Arabidopsis thaliana

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 54–882	Not recorded	Isoamylase 1, chloroplastic × 2 （O04196）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.38 Å

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 9XVP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9XVI Arabidopsis ISA2-ISA1-ISA1-ISA2 heterotetramer Deposited 2025-11-26	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 54–882（829 aa） Chain D 54–882（829 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.65 Å
9XVV Maltoheptaose-bound Arabidopsis ISA2-ISA1-ISA1 heterotrimer Deposited 2025-11-27	Different oligomeric state Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 54–882（829 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.49 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ISOA2_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain C； PDBConstruct 42–870； UniProt 54–882

Isoamylase 1, chloroplastic

Arabidopsis thaliana

UniProt O04196

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 44–783 Chain B； UniProt 44–783	Not recorded	Isoamylase 2, chloroplastic × 1 （Q8L735）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.38 Å

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 9XVP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9XVE Arabidopsis ISA1-ISA1 homodimer Deposited 2025-11-26	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 44–783（740 aa） Chain B 44–783（740 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.36 Å
9XVG Maltoheptaose-incubated Arabidopsis ISA1-ISA1 homodimer Deposited 2025-11-26	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 44–783（740 aa） Chain B 44–783（740 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.49 Å
9XVI Arabidopsis ISA2-ISA1-ISA1-ISA2 heterotetramer Deposited 2025-11-26	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 44–783（740 aa） Chain B 44–783（740 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.65 Å
9XVV Maltoheptaose-bound Arabidopsis ISA2-ISA1-ISA1 heterotrimer Deposited 2025-11-27	Different oligomeric state Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 44–783（740 aa） Chain B 44–783（740 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.49 Å

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

View Construct and Data Evidence

UniProt name	ISOA1_ARATH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 25–764； UniProt 44–783 Author chain B； PDBConstruct 25–764； UniProt 44–783

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	9xvp
Deposition date deposition_date	2025-11-26
Structure title title	Arabidopsis ISA2-ISA1-ISA1 heterotrimer
Keywords keywords	isoamylase, ISA1, ISA2, PLANT PROTEIN; PLANT PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	57.09 Å
Radius of gyration Rg (electron density) rg_electron	58.30 Å
Forward intensity I(0) i0	795352000.00
Molecular weight molecular_weight	234040.0 kDa
Excluded volume excluded_volume	292250 Å³
Envelope volume envelope_volume	424350 Å³
Hydration-shell volume shell_volume	68793 Å³
Envelope diameter envelope_diameter	225.3 Å
Shell Rg shell_rg	50.03 Å
Envelope Rg envelope_rg	58.83 Å
Shape Rg shape_rg	58.28 Å
Total Rg total_rg	58.10 Å
Total atoms total_atoms	16512
Residues n_residues	2054
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	210.0 Å
Rg (real space) rg_real	58.15 Å
Rg uncertainty (real space) rg_real_error	2.52 Å
I(0) (real space) i0_real	7.9530e+08
I(0) uncertainty (real space) i0_real_error	1.6030e+07
Rg (reciprocal space) rg_reciprocal	56.20 Å
I(0) (reciprocal space) i0_reciprocal	793000000.0000
Solution quality estimate total_estimate	0.7043
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	45.0 Å
Skewness Skewness skewness	0.723
Kurtosis Kurtosis kurtosis	-0.097
Angular range angular_range	— – 0.1400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	84960000.0000
Real-space data points n_real_points	29
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.411; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.402; Smooth: 0.518

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Isoamylase 2, chloroplastic
Molecular weight formula_weight	97595.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C
Atom count atom_count	16512

MDYKDDDDKWSHPQFEKGGGGSGGSAWSHPQFEKEFKGLVDGDLVTSALQSYQFSKICASKTSIELREALSSRRAEADDLKKVTSYSFRTKAGALVKVKVEKKREKYSILVYVSSLELSGDDKSRLVMVWGVYRSDSSCFLPLDFENSSQDSQTHTTETTFVKSSLSELMLGLEFDGKESPFYLSFHLKLVSGRDPDGQEMLTHRDTDFCIPVGFTAGHPLPLGLSSGPDDDSWNFSFFSRSSTNVVLCLYDDSTTDKPALELDLDPYVNRTGDVWHASVDNTWDFVRYGYRCKETAHSKEDVDVEGEPIVLDPYATVVGKSVSQKYLGSLSKSPSFDWGEDVSPNIPLEKLLVYRLNVKGFTQHRSSKLPSNVAGTFSGVAEKVSHLKTLGTNAVLLEPIFSFSEQKGPYFPFHFFSPMDIYGPSNSLESAVNSMKVMVKKLHSEGIEVLLEVVFTHTADSGALRGIDDSSYYYKGRANDLDSKSYLNCNYPVVQQLVLESLRYWVTEFHVDGFCFINASSLLRGVHGEQLSRPPLVEAIAFDPLLAETKLIADCWDPLEMMPKEVRFPHWKRWAELNTRYCRNVRNFLRGRGVLSDLATRICGSGDVFTDGRGPAFSFNYISRNSGLSLVDIVSFSGPELASELSWNCGEEGATNKSAVLQRRLKQIRNFLFIQYISLGVPVLNMGDECGISTRGSPLLESRKPFDWNLLASAFGTQITQFISFMTSVRARRSDVFQRRDFLKPENIVWYANDQTTPKWEDPASKFLALEIKSESEEEETASLAEPNEPKSNDLFIGFNASDHPESVVLPSLPDGSKWRRLVDTALPFPGFFSVEGETVVAEEPLQQLVVYEMKPYSCTLFETINTTA

来源 Source

来源生物 organism	Arabidopsis thaliana
通用名 common_name	thale cress
NCBI Class编号 ncbi_taxonomy_id	3702
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Isoamylase 1, chloroplastic
Molecular weight formula_weight	87301.9 kDa
EC 编号 ec_number	3.2.1.68
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B

MAHHHHHHHHHHGSGSGSGSGSEFAKDRRSNEAENIAVVEKPLKSDRFFISDGLPSPFGPTVRDDGVNFSVYSTNSVSATICLISLSDLRQNKVTEEIQLDPSRNRTGHVWHVFLRGDFKDMLYGYRFDGKFSPEEGHYYDSSNILLDPYAKAIISRDEFGVLGPDDNCWPQMACMVPTREEEFDWEGDMHLKLPQKDLVIYEMHVRGFTRHESSKIEFPGTYQGVAEKLDHLKELGINCIELMPCHEFNELEYYSYNTILGDHRVNFWGYSTIGFFSPMIRYASASSNNFAGRAINEFKILVKEAHKRGIEVIMDVVLNHTAEGNEKGPIFSFRGVDNSVYYMLAPKGEFYNYSGCGNTFNCNHPVVRQFILDCLRYWVTEMHVDGFRFDLGSIMSRSSSLWDAANVYGADVEGDLLTTGTPISCPPVIDMISNDPILRGVKLIAEAWDAGGLYQVGMFPHWGIWSEWNGKFRDVVRQFIKGTDGFSGAFAECLCGSPNLYQGGRKPWHSINFICAHDGFTLADLVTYNNKNNLANGEENNDGENHNYSWNCGEEGDFASISVKRLRKRQMRNFFVSLMVSQGVPMIYMGDEYGHTKGGNNNTYCHDNYMNYFRWDKKEEAHSDFFRFCRILIKFRDECESLGLNDFPTAKRLQWHGLAPEIPNWSETSRFVAFSLVDSVKKEIYVAFNTSHLATLVSLPNRPGYRWEPFVDTSKPSPYDCITPDLPERETAMKQYRHFLDANVYPMLSYSSIILLLSPIKDP

来源 Source

来源生物 organism	Arabidopsis thaliana
通用名 common_name	thale cress
NCBI Class编号 ncbi_taxonomy_id	3702
宿主生物 host_organism	Homo sapiens

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	3.380 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.38 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	300200

fit	/app/data/saxs_computation/xv/9xvp/9xvp.fit
pddf	/app/data/pr_computation/xv/9xvp/9xvp.pr.out
profile	/app/data/saxs_computation/xv/9xvp/9xvp.dat

Arabidopsis ISA2-ISA1-ISA1 heterotrimer

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

Isoamylase 2, chloroplastic

State in the Current Structure

Other States of the Same Protein in the Database

Isoamylase 1, chloroplastic

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)