SAXSdb — 9y9w

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

Cadherin domain protein

Vibrio cholerae O395

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 × 12 PDB declaration: 12-meric（12） Consistent with protein copy count	Chain A； UniProt 1119–1460 Chain B； UniProt 1119–1460 Chain E； UniProt 1119–1460 Chain G； UniProt 1119–1460 Chain I； UniProt 1119–1460 Chain K； UniProt 1119–1460	Not recorded	Ala-Gly-Trp-Thr-Asp (AGWTD) × 6 CA CALCIUM ION × 36 PEG DI(HYDROXYETHYL)ETHER × 2 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions：MICROBATCH；pH 9；293 K；0.16 M calcium acetate, 0.08 M sodium cacodylate, and 24.4% (w/v) PEG 8000. Ethylene glycol was used as a cryoprotectant.	Resolution 2.40 Å R-free 0.232

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 9Y9W	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9YBQ Vibrio cholerae protein FrhA peptid-binding domain and adjacent split domain (S1127-F1439) in complex with peptide AGYTD X-ray crystallography structure Deposited 2025-09-17	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric	Chain A 1119–1460（342 aa） Chain B 1119–1460（342 aa） Chain E 1119–1460（342 aa） Chain G 1119–1460（342 aa） Chain I 1119–1460（342 aa） Chain K 1119–1460（342 aa）	Not recorded	CA CALCIUM ION × 36	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 9；293 K；0.16 M calcium acetate, 0.08 M sodium cacodylate, and 24.4% (w/v) PEG 8000. Ethylene glycol was used as a cryoprotectant.	Resolution 2.50 Å R-free 0.252

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A0H3AMP4_VIBC3
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–363； UniProt 1119–1460 Author chain B； PDBConstruct 22–363； UniProt 1119–1460 Author chain E； PDBConstruct 22–363； UniProt 1119–1460 Author chain G； PDBConstruct 22–363； UniProt 1119–1460 Author chain I； PDBConstruct 22–363； UniProt 1119–1460 Author chain K； PDBConstruct 22–363； UniProt 1119–1460

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	9y9w
Deposition date deposition_date	2025-09-15
Structure title title	Vibrio cholerae protein FrhA peptid-binding domain and adjacent split domain (S1127-F1439) in complex with peptide AGWTD X-ray crystallography structure
Keywords keywords	Calcium, Adhesin, RTX, peptide-binding domain, split domain, Inhibitor, METAL BINDING PROTEIN; METAL BINDING PROTEIN
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	45.84 Å
Radius of gyration Rg (electron density) rg_electron	45.77 Å
Forward intensity I(0) i0	621284000.00
Molecular weight molecular_weight	197060.0 kDa
Excluded volume excluded_volume	242390 Å³
Envelope volume envelope_volume	336810 Å³
Hydration-shell volume shell_volume	62958 Å³
Envelope diameter envelope_diameter	169.2 Å
Shell Rg shell_rg	48.80 Å
Envelope Rg envelope_rg	44.83 Å
Shape Rg shape_rg	45.74 Å
Total Rg total_rg	45.98 Å
Total atoms total_atoms	13827
Residues n_residues	1869
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	161.1 Å
Rg (real space) rg_real	46.11 Å
Rg uncertainty (real space) rg_real_error	2.49 Å
I(0) (real space) i0_real	6.2130e+08
I(0) uncertainty (real space) i0_real_error	1.3800e+07
Rg (reciprocal space) rg_reciprocal	45.85 Å
I(0) (reciprocal space) i0_reciprocal	621100000.0000
Solution quality estimate total_estimate	0.8532
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	47.4 Å
Skewness Skewness skewness	0.479
Kurtosis Kurtosis kurtosis	-0.316
Angular range angular_range	— – 0.1700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	54910000.0000
Real-space data points n_real_points	35
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.757; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.838

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Cadherin domain protein
Molecular weight formula_weight	38041.1 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,E,G,I,K
Atom count atom_count	15182

MASSHHHHHHSSGLVPRGSHMTVIDVDGSQITDSLDVKIVDDASTALDDRGEVDIVADSFTVSGVVANWTSWSNGTNVTTFDGTNAPNGGGLDNDSGKDQIRWGQPASSYSSGYGFIDNDSALNGEFALNQDIILGTFTHYNYPVYSGGAITSASMDVAFSVTDAHGVLTPVTLKLNFDHNETPNTNNPEASKDIIKVGNTNVTFENAGALYTLQVIGFRIPGTNQIVTEIRTGENATNSYELVVRVGPGEGYELPSTSGNVLSNDVSGADVDMTVVGAASGNHVSSGVSGSVGSMIAGLYGNLILLADGSYTYQVTANASSIPNDAIEIFTYTMKDGDGDTSTALLSINVNRVTMADFNANQ

来源 Source

来源生物 organism	Vibrio cholerae O395
NCBI Class编号 ncbi_taxonomy_id	345073
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Ala-Gly-Trp-Thr-Asp (AGWTD)
Molecular weight formula_weight	548.5 kDa
Source method src_method	syn
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,N,O,P,Q,R

AGWTD

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	man
Copy count entity_count	36

来源 Source

来源生物 organism	Vibrio cholerae O395
NCBI Class编号 ncbi_taxonomy_id	345073
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	man
Copy count entity_count	5

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1348

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8. Citations (2)

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Unit-cell length a length_a	61.273 Å
Unit-cell length b length_b	118.726 Å
Unit-cell length c length_c	118.706 Å
Unit-cell angle α angle_alpha	60.03 °
Unit-cell angle β angle_beta	85.62 °
Unit-cell angle γ angle_gamma	76.70 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	102.720 Å
R factor r_factor	0.2270
R_work r_work	0.2270
R_free r_free	0.2318

fit	/app/data/saxs_computation/y9/9y9w/9y9w.fit
pddf	/app/data/pr_computation/y9/9y9w/9y9w.pr.out
profile	/app/data/saxs_computation/y9/9y9w/9y9w.dat

Vibrio cholerae protein FrhA peptid-binding domain and adjacent split domain (S1127-F1439) in complex with peptide AGWTD X-ray crystallography structure

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

Cadherin domain protein

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

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)