5mts

Complex of FimH lectin with a TazMan (thiazolylaminomannosides) family member known as potent anti-adhesive agent at 2.6 A resolution

Method: X-RAY DIFFRACTION Dmax: 89.0 Å Quality: GOOD

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

Protein FimH

Escherichia coli K-12

UniProt P08191

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 1–300 Not recorded XKA [2-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]amino]-1,3-thiazol-5-yl]-(4-methyl-2-pyrazin-2-yl-1,3-thiazol-5-yl)methanone × 1 NI NICKEL (II) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;300 K;1.0 M LI2SO4 0.1 M TRIS-HCL 0.01 M NICL2 3% GLYCEROL Resolution 2.60 Å R-free 0.250
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1–300 Not recorded XKA [2-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]amino]-1,3-thiazol-5-yl]-(4-methyl-2-pyrazin-2-yl-1,3-thiazol-5-yl)methanone × 1 NI NICKEL (II) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;300 K;1.0 M LI2SO4 0.1 M TRIS-HCL 0.01 M NICL2 3% GLYCEROL Resolution 2.60 Å R-free 0.250

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.

57 other PDB entries and 137 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FIMH_ECOLI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–300; UniProt 1–300 Author chain B; PDBConstruct 1–300; UniProt 1–300

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.

SAXS scattering curve SAXS Profile

SAXS profile for 5mts

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5mts
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5mts
Deposition date deposition_date2017-01-10
Structure title titleComplex of FimH lectin with a TazMan (thiazolylaminomannosides) family member known as potent anti-adhesive agent at 2.6 A resolution
Keywords keywords;CELL ADHESION, BACTERIAL ADHESIN, TYPE 1 FIMBRIAE, URINARY TRACT INFECTION, CROHN'S DISEASE ;; CELL ADHESION
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier24.64
Radius of gyration Rg (electron density) rg_electron23.60
Forward intensity I(0) i020558100.00
Molecular weight molecular_weight34828.0 kDa
Excluded volume excluded_volume43523 ų
Envelope volume envelope_volume50653 ų
Hydration-shell volume shell_volume19319 ų
Envelope diameter envelope_diameter93.4
Shell Rg shell_rg28.73
Envelope Rg envelope_rg23.59
Shape Rg shape_rg23.57
Total Rg total_rg24.28
Total atoms total_atoms2454
Residues n_residues316
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax89.0
Rg (real space) rg_real24.84
Rg uncertainty (real space) rg_real_error0.87
I(0) (real space) i0_real2.0560e+07
I(0) uncertainty (real space) i0_real_error3.1310e+05
Rg (reciprocal space) rg_reciprocal24.79
I(0) (reciprocal space) i0_reciprocal20560000.0000
Solution quality estimate total_estimate0.8170
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.6
Skewness Skewness skewness0.483
Kurtosis Kurtosis kurtosis-0.262
Angular range angular_range— – 0.3200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4567000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.726; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.548; Smooth: 0.891

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd5mtsa_
Class classb — All beta proteins
Fold Fold foldb.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamilyb.2.3 — Bacterial adhesins
Family Family familyb.2.3.2 — Pilus subunits
Domain ID domain_idd5mtsb_
Class classb — All beta proteins
Fold Fold foldb.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamilyb.2.3 — Bacterial adhesins
Family Family familyb.2.3.2 — Pilus subunits

CATH v4.4 (2 domains)

Domain ID domain_id5mtsA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1090 — Fimbrial-type adhesion domain
Domain ID domain_id5mtsB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1090 — Fimbrial-type adhesion domain

8. Citations (1)

9. Files and Curves (10)