SAXSdb — 4xoc

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

FimH protein

Escherichia coli O6:K15:H31

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 25–183	Fragment：UNP residues 25-183	KGM heptyl alpha-D-mannopyranoside × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；17 % PEG2000MME, 0.1M Hepes pH 7.5	Resolution 1.42 Å R-free 0.174
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 25–183	Fragment：UNP residues 25-183	KGM heptyl alpha-D-mannopyranoside × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；17 % PEG2000MME, 0.1M Hepes pH 7.5	Resolution 1.42 Å R-free 0.174

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 4XOC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3JWN Complex of FimC, FimF, FimG and FimH Deposited 2009-09-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain H 25–303（279 aa） Fragment：UNP residues 25-303	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.1；293 K；1.6 M potassium chloride, 0.1 M sodium citrate, pH 4.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.69 Å R-free 0.272
3JWN Complex of FimC, FimF, FimG and FimH Deposited 2009-09-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain N 25–303（279 aa） Fragment：UNP residues 25-303	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.1；293 K；1.6 M potassium chloride, 0.1 M sodium citrate, pH 4.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.69 Å R-free 0.272
4XOD Crystal structure of a FimH*DsG complex from E.coli F18 Deposited 2015-01-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 25–303（279 aa） Fragment：UNP residues 25-303	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；25 % (w/v) PEG 3350, 0.2 M magnesium chloride, 0.1 M BisTris-HCl pH 5.5	Resolution 1.14 Å R-free 0.159
4XOE Crystal structure of a FimH*DsG complex from E.coli F18 with bound heptyl alpha-D-mannopyrannoside Deposited 2015-01-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 25–303（279 aa） Fragment：UNP residues 25-303	Not recorded	KGM heptyl alpha-D-mannopyranoside × 1 CAC CACODYLATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；30 % (v/v) 2-Methyl-2,4-pentanediol (MPD), 0.1 M sodium cacodylate, 0.2 M magnesium acetate pH 6.5	Resolution 2.40 Å R-free 0.179

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

View Construct and Data Evidence

UniProt name	Q0T8Y8_ECOL5
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–159； UniProt 25–183 Author chain B； PDBConstruct 1–159； UniProt 25–183

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	4xoc
Deposition date deposition_date	2015-01-16
Structure title title	Crystal structure of the FimH lectin domain from E.coli F18 in complex with heptyl alpha-D-mannopyrannoside
Keywords keywords	type I pilus, catch-bond, cell adhesion, lectin, UPEC, bacterial adhesin, UTI, mannose, isomerase; 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	23.86 Å
Radius of gyration Rg (electron density) rg_electron	23.06 Å
Forward intensity I(0) i0	19484000.00
Molecular weight molecular_weight	34355.0 kDa
Excluded volume excluded_volume	43224 Å³
Envelope volume envelope_volume	50192 Å³
Hydration-shell volume shell_volume	19290 Å³
Envelope diameter envelope_diameter	78.3 Å
Shell Rg shell_rg	28.42 Å
Envelope Rg envelope_rg	22.99 Å
Shape Rg shape_rg	23.05 Å
Total Rg total_rg	23.75 Å
Total atoms total_atoms	4806
Residues n_residues	317
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	77.3 Å
Rg (real space) rg_real	23.92 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	1.9480e+07
I(0) uncertainty (real space) i0_real_error	2.6840e+05
Rg (reciprocal space) rg_reciprocal	23.91 Å
I(0) (reciprocal space) i0_reciprocal	19480000.0000
Solution quality estimate total_estimate	0.8913
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	76.1 Å
Skewness Skewness skewness	0.318
Kurtosis Kurtosis kurtosis	-0.618
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3803000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.910; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.884; Smooth: 0.970

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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	FimH protein
Molecular weight formula_weight	16945.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5540

FACKTANGTAIPIGGGSANVYVNLAPAVNVGQNLVVDLSTQIFCHNDYPETITDYVTLQRGSAYGGVLSSFSGTVKYNGSSYPFPTTSETPRVVYNSRTDKPWPVALYLTPVSSAGGVAIKAGSLIAVLILRQTNNYNSDDFQFVWNIYANNDVVVPTG

来源 Source

来源生物 organism	Escherichia coli O6:K15:H31
NCBI Class编号 ncbi_taxonomy_id	362663
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	heptyl alpha-D-mannopyranoside
Molecular weight formula_weight	278.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	596

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4xoca_
Class class	b — All beta proteins
Fold Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamily	b.2.3 — Bacterial adhesins
Family Family family	b.2.3.2 — Pilus subunits

Domain ID domain_id	d4xocb_
Class class	b — All beta proteins
Fold Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamily	b.2.3 — Bacterial adhesins
Family Family family	b.2.3.2 — Pilus subunits

CATH v4.4 (2 domains)

Domain ID domain_id	4xocA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1090 — Fimbrial-type adhesion domain

Domain ID domain_id	4xocB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1090 — Fimbrial-type adhesion domain

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8. Citations (1)

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Unit-cell length a length_a	140.070 Å
Unit-cell length b length_b	176.056 Å
Unit-cell length c length_c	28.330 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	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.420 Å
Low-resolution limit resolution_low	54.806 Å
R factor r_factor	0.1496
R_work r_work	0.1483
R_free r_free	0.1745

fit	/app/data/saxs_computation/xo/4xoc/4xoc.fit
pddf	/app/data/pr_computation/xo/4xoc/4xoc.pr.out
profile	/app/data/saxs_computation/xo/4xoc/4xoc.dat

Crystal structure of the FimH lectin domain from E.coli F18 in complex with heptyl alpha-D-mannopyrannoside

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

FimH 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