SAXSdb — 1ay2

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

TYPE 4 PILIN

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	Other combination Homooligomer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 8–165	Not recorded	alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 PT PLATINUM (II) ION × 2 HTO HEPTANE-1,2,3-TRIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；PROTEIN WAS CRYSTALLIZED FROM 60% PEG400, 50 MM CHESS, PH 8.0, 1% BETA-OCTYL GLUCOSIDE, 0.6% 1,2,3-HEPTANETRIOL.	Resolution 2.60 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 1AY2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2HI2 Crystal structure of native Neisseria gonorrhoeae Type IV pilin at 2.3 Angstroms Resolution Deposited 2006-06-28	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 8–165（158 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HTO HEPTANE-1,2,3-TRIOL × 1 OPE PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；298 K；22% PEG 400 5% HEPTANE TRIOL 50 mM CHES, PH 8.0, VAPOR DIFFUSION, TEMPERATURE 298K	Resolution 2.30 Å R-free 0.282
2HIL Structure of the Neisseria gonorrhoeae Type IV pilus filament from x-ray crystallography and electron cryomicroscopy Deposited 2006-06-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 18 PDB declaration: octadecameric	Chain A 8–165（158 aa） Chain B 8–165（158 aa） Chain C 8–165（158 aa） Chain D 8–165（158 aa） Chain E 8–165（158 aa） Chain F 8–165（158 aa） Chain G 8–165（158 aa） Chain H 8–165（158 aa） Chain I 8–165（158 aa） Chain J 8–165（158 aa） Chain K 8–165（158 aa） Chain L 8–165（158 aa） Chain M 8–165（158 aa） Chain N 8–165（158 aa） Chain O 8–165（158 aa） Chain P 8–165（158 aa） Chain Q 8–165（158 aa） Chain R 8–165（158 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	OPE PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER × 18	ELECTRON MICROSCOPY cryo-EM buffer 50 mM CHES；pH 9.5；50 mM CHES cryo-EM vitrification conditions Cryogen ETHANE；5 ul of sample were applied to grids for 1 minute, blotted for 2.5 seconds then plunge-frozen in liquid ethane using an FEI Vitrobot	Resolution 12.50 Å
2PIL Crystallographic Structure of Phosphorylated Pilin from Neisseria: Phosphoserine Sites Modify Type IV Pilus Surface Chemistry Deposited 1998-03-02	Different mutation/modification Different oligomeric state Different ligand/ion	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 8–165（158 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	PT PLATINUM (II) ION × 1 HTO HEPTANE-1,2,3-TRIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；PROTEIN WAS CRYSTALLIZED FROM 60% PEG400, 50 MM CHESS, PH 8.0, 1% BETA-OCTYL GLUCOSIDE, 0.6% 1,2,3-HEPTANETRIOL.	Resolution 2.60 Å
5VXX Cryo-EM reconstruction of Neisseria gonorrhoeae Type IV pilus Deposited 2017-05-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 21 PDB declaration: 21-meric	Chain A 8–165（158 aa） Chain B 8–165（158 aa） Chain C 8–165（158 aa） Chain D 8–165（158 aa） Chain E 8–165（158 aa） Chain F 8–165（158 aa） Chain G 8–165（158 aa） Chain H 8–165（158 aa） Chain I 8–165（158 aa） Chain J 8–165（158 aa） Chain K 8–165（158 aa） Chain L 8–165（158 aa） Chain M 8–165（158 aa） Chain N 8–165（158 aa） Chain O 8–165（158 aa） Chain P 8–165（158 aa） Chain Q 8–165（158 aa） Chain R 8–165（158 aa） Chain S 8–165（158 aa） Chain T 8–165（158 aa） Chain U 8–165（158 aa）	Mutation：P69S, S71T Mutation：P69S, S71T Mutation：P69S, S71T Mutation：P69S, S71T Mutation：P69S, S71T Mutation：P69S, S71T Mutation：P69S, S71T Mutation：P69S, S71T Mutation：P69S, S71T Mutation：P69S, S71T Mutation：P69S, S71T Mutation：P69S, S71T Mutation：P69S, S71T Mutation：P69S, S71T Mutation：P69S, S71T Mutation：P69S, S71T Mutation：P69S, S71T Mutation：P69S, S71T Mutation：P69S, S71T Mutation：P69S, S71T Mutation：P69S, S71T	OPE PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER × 21	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；PBS buffer cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.10 Å

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

View Construct and Data Evidence

UniProt name	FMM1_NEIGO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–158； UniProt 8–165

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	1ay2
Deposition date deposition_date	1997-11-13
Structure title title	STRUCTURE OF THE FIBER-FORMING PROTEIN PILIN AT 2.6 ANGSTROMS RESOLUTION
Keywords keywords	TYPE IV PILIN, FIBER-FORMING PROTEIN, MEMBRANE PROTEIN, DNA INDING PROTEIN, CONTRACTILE PROTEIN, CELL ADHESION; CELL ADHESION
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	19.55 Å
Radius of gyration Rg (electron density) rg_electron	21.60 Å
Forward intensity I(0) i0	6107940.00
Molecular weight molecular_weight	17881.0 kDa
Excluded volume excluded_volume	22258 Å³
Envelope volume envelope_volume	27590 Å³
Hydration-shell volume shell_volume	13154 Å³
Envelope diameter envelope_diameter	94.2 Å
Shell Rg shell_rg	23.30 Å
Envelope Rg envelope_rg	24.80 Å
Shape Rg shape_rg	21.45 Å
Total Rg total_rg	22.29 Å
Total atoms total_atoms	1244
Residues n_residues	158
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	51.8 Å
Rg (real space) rg_real	17.21 Å
Rg uncertainty (real space) rg_real_error	0.11 Å
I(0) (real space) i0_real	5.7340e+06
I(0) uncertainty (real space) i0_real_error	5.8040e+04
Rg (reciprocal space) rg_reciprocal	20.29 Å
I(0) (reciprocal space) i0_reciprocal	6107000.0000
Solution quality estimate total_estimate	0.6780
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.7 Å
Skewness Skewness skewness	0.420
Kurtosis Kurtosis kurtosis	-0.232
Angular range angular_range	— – 0.4050 Å⁻¹
Current regularization parameter α current_alpha	2.0430
Highest regularization parameter α highest_alpha	832200.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.041; Oscil: 0.952; Stabil: 0.990; Sysdev: 0.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	TYPE 4 PILIN
Molecular weight formula_weight	17192.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1373

FTLIELMIVIAIVGILAAVALPAYQDYTARAQVSEAILLAEGQKSAVTEYYLNHGKWPENNTSAGVASPPSDIKGKYVKEVEVKNGVVTATMLSSGVNNEIKGKKLSLWARRENGSVKWFCGQPVTRTDDDTVADAKDGKEIDTKHLPSTCRDNFDAK

Entity 2 Entity 2 branched

Description description	alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	383.3 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	PLATINUM (II) ION
Molecular weight formula_weight	195.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	HEPTANE-1,2,3-TRIOL
Molecular weight formula_weight	148.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	129

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1ay2a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.24 — Pili subunits
Superfamily Superfamily superfamily	d.24.1 — Pili subunits
Family Family family	d.24.1.1 — Pilin

CATH v4.4 (1 domains)

Domain ID domain_id	1ay2A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	700 — Glycoprotein, Type 4 Pilin
Homologous superfamily homologous superfamily	10 — Glycoprotein, Type 4 Pilin

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8. Citations (1)

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Unit-cell length a length_a	127.580 Å
Unit-cell length b length_b	121.080 Å
Unit-cell length c length_c	26.860 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 2
Space-group number int_tables_number	21
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1940
R_work r_work	0.1940
R_free r_free	—

fit	/app/data/saxs_computation/ay/1ay2/1ay2.fit
pddf	/app/data/pr_computation/ay/1ay2/1ay2.pr.out
profile	/app/data/saxs_computation/ay/1ay2/1ay2.dat

STRUCTURE OF THE FIBER-FORMING PROTEIN PILIN AT 2.6 ANGSTROMS RESOLUTION

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

TYPE 4 PILIN

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