SAXSdb — 9ydx

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

Flagellar M-ring protein

OrganismNot specified

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 homooligomer Homooligomer Protein × 34 PDB declaration: 34-meric（34） Consistent with protein copy count	Chain Aa； UniProt 256–453 Chain Ab； UniProt 256–453 Chain Ac； UniProt 256–453 Chain Ad； UniProt 256–453 Chain Ae； UniProt 256–453 Chain Af； UniProt 256–453 Chain Ag； UniProt 256–453 Chain Ah； UniProt 256–453 Chain Ai； UniProt 256–453 Chain Aj； UniProt 256–453 Chain Ak； UniProt 256–453 Chain Al； UniProt 256–453 Chain Am； UniProt 256–453 Chain An； UniProt 256–453 Chain Ao； UniProt 256–453 Chain Ap； UniProt 256–453 Chain Aq； UniProt 256–453 Chain Ar； UniProt 256–453 Chain As； UniProt 256–453 Chain At； UniProt 256–453 Chain Au； UniProt 256–453 Chain Av； UniProt 256–453 Chain Aw； UniProt 256–453 Chain Ax； UniProt 256–453 Chain Ay； UniProt 256–453 Chain Az； UniProt 256–453 Chain Ba； UniProt 256–453 Chain Bb； UniProt 256–453 Chain Bc； UniProt 256–453 Chain Bd； UniProt 256–453 Chain Be； UniProt 256–453 Chain Bf； UniProt 256–453 Chain Bg； UniProt 256–453 Chain Bh； UniProt 256–453	Not recorded	No other associated polymer	ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions	Resolution 3.75 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 9YDX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9YH7 Composite structure of the sheathed flagellar motor in Vibrio cholerae adopting a higher FOMC conformation Deposited 2025-09-30	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 407 PDB declaration: 407-meric	Chain Oj 256–453（198 aa） Chain Ok 256–453（198 aa） Chain Ol 256–453（198 aa） Chain Om 256–453（198 aa） Chain On 256–453（198 aa） Chain Oo 256–453（198 aa） Chain Op 256–453（198 aa） Chain Oq 256–453（198 aa） Chain Or 256–453（198 aa） Chain Os 256–453（198 aa） Chain Ot 256–453（198 aa） Chain Ou 256–453（198 aa） Chain Ov 256–453（198 aa） Chain Ow 256–453（198 aa） Chain Ox 256–453（198 aa） Chain Oy 256–453（198 aa） Chain Oz 256–453（198 aa） Chain Pa 256–453（198 aa） Chain Pb 256–453（198 aa） Chain Pc 256–453（198 aa） Chain Pd 256–453（198 aa） Chain Pe 256–453（198 aa） Chain Pf 256–453（198 aa） Chain Pg 256–453（198 aa） Chain Ph 256–453（198 aa） Chain Pi 256–453（198 aa） Chain Pj 256–453（198 aa） Chain Pk 256–453（198 aa） Chain Pl 256–453（198 aa） Chain Pm 256–453（198 aa） Chain Pn 256–453（198 aa） Chain Po 256–453（198 aa） Chain Pp 256–453（198 aa） Chain Pq 256–453（198 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.60 Å

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

View Construct and Data Evidence

UniProt name	Q9KQ69_VIBCH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain Aa； PDBConstruct 1–198； UniProt 256–453 Author chain Ab； PDBConstruct 1–198； UniProt 256–453 Author chain Ac； PDBConstruct 1–198； UniProt 256–453 Author chain Ad； PDBConstruct 1–198； UniProt 256–453 Author chain Ae； PDBConstruct 1–198； UniProt 256–453 Author chain Af； PDBConstruct 1–198； UniProt 256–453 Author chain Ag； PDBConstruct 1–198； UniProt 256–453 Author chain Ah； PDBConstruct 1–198； UniProt 256–453 Author chain Ai； PDBConstruct 1–198； UniProt 256–453 Author chain Aj； PDBConstruct 1–198； UniProt 256–453 Author chain Ak； PDBConstruct 1–198； UniProt 256–453 Author chain Al； PDBConstruct 1–198； UniProt 256–453 Author chain Am； PDBConstruct 1–198； UniProt 256–453 Author chain An； PDBConstruct 1–198； UniProt 256–453 Author chain Ao； PDBConstruct 1–198； UniProt 256–453 Author chain Ap； PDBConstruct 1–198； UniProt 256–453 Author chain Aq； PDBConstruct 1–198； UniProt 256–453 Author chain Ar； PDBConstruct 1–198； UniProt 256–453 Author chain As； PDBConstruct 1–198； UniProt 256–453 Author chain At； PDBConstruct 1–198； UniProt 256–453 Author chain Au； PDBConstruct 1–198； UniProt 256–453 Author chain Av； PDBConstruct 1–198； UniProt 256–453 Author chain Aw； PDBConstruct 1–198； UniProt 256–453 Author chain Ax； PDBConstruct 1–198； UniProt 256–453 Author chain Ay； PDBConstruct 1–198； UniProt 256–453 Author chain Az； PDBConstruct 1–198； UniProt 256–453 Author chain Ba； PDBConstruct 1–198； UniProt 256–453 Author chain Bb； PDBConstruct 1–198； UniProt 256–453 Author chain Bc； PDBConstruct 1–198； UniProt 256–453 Author chain Bd； PDBConstruct 1–198； UniProt 256–453 Author chain Be； PDBConstruct 1–198； UniProt 256–453 Author chain Bf； PDBConstruct 1–198； UniProt 256–453 Author chain Bg； PDBConstruct 1–198； UniProt 256–453 Author chain Bh； PDBConstruct 1–198； UniProt 256–453

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	9ydx
Deposition date deposition_date	2025-09-23
Structure title title	RBM3 domain of FliF protein in MS-ring of flagellar motor in Vibrio cholerae
Keywords keywords	In situ cryo-EM, sheathed flagellar motor, Vibrio cholerae, MS-ring, FliF, assembled state, MOTOR PROTEIN; MOTOR 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	83.61 Å
Radius of gyration Rg (electron density) rg_electron	84.29 Å
Forward intensity I(0) i0	4377160000.00
Molecular weight molecular_weight	547430.0 kDa
Excluded volume excluded_volume	680400 Å³
Envelope volume envelope_volume	1418300 Å³
Hydration-shell volume shell_volume	148010 Å³
Envelope diameter envelope_diameter	231.0 Å
Shell Rg shell_rg	86.00 Å
Envelope Rg envelope_rg	73.74 Å
Shape Rg shape_rg	84.22 Å
Total Rg total_rg	84.56 Å
Total atoms total_atoms	38556
Residues n_residues	4896
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	217.5 Å
Rg (real space) rg_real	83.19 Å
Rg uncertainty (real space) rg_real_error	0.93 Å
I(0) (real space) i0_real	4.3760e+09
I(0) uncertainty (real space) i0_real_error	7.8170e+07
Rg (reciprocal space) rg_reciprocal	84.47 Å
I(0) (reciprocal space) i0_reciprocal	4388000000.0000
Solution quality estimate total_estimate	0.8459
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	137.4 Å
Skewness Skewness skewness	-0.120
Kurtosis Kurtosis kurtosis	-0.871
Angular range angular_range	— – 0.0950 Å⁻¹
Current regularization parameter α current_alpha	0.0025
Highest regularization parameter α highest_alpha	117700000.0000
Real-space data points n_real_points	20
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.998; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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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	triclinic

Resolution resolution	3.75 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	44428

Description description	Flagellar M-ring protein
Molecular weight formula_weight	21495.8 kDa
Source method src_method	nat
Copy count entity_count	34

Polymer type type	polypeptide(L)
Chain IDs strand_id	Aa,Ab,Ac,Ad,Ae,Af,Ag,Ah,Ai,Aj,Ak,Al,Am,An,Ao,Ap,Aq,Ar,As,At,Au,Av,Aw,Ax,Ay,Az,Ba,Bb,Bc,Bd,Be,Bf,Bg,Bh
Atom count atom_count	38556

RBM3 domain of FliF protein in MS-ring of flagellar motor in Vibrio cholerae

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

Flagellar M-ring 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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/yd/9ydx/9ydx.fit
pddf	/app/data/pr_computation/yd/9ydx/9ydx.pr.out
profile	/app/data/saxs_computation/yd/9ydx/9ydx.dat