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4e1t

X-ray crystal structure of the transmembrane beta-domain from invasin from Yersinia pseudotuberculosis

Method: X-RAY DIFFRACTION Dmax: 63.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Invasin

Yersinia pseudotuberculosis

UniProt P11922

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 147–390 Fragment：transmembrane domain (UNP residues 147-390) Mutation：L352F OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 12 OLB (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1 X-RAY DIFFRACTION X-ray crystallization conditions：LIPIDIC CUBIC PHASE MONOOLEIN；pH 4；294 K；0.05 M sodium citrate, pH 3.8-4.4, 0.2 M lithium sulfate, 23-35% PEG400, LIPIDIC CUBIC PHASE MONOOLEIN, temperature 294K Resolution 2.26 Å R-free 0.260

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 4E1T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CWV CRYSTAL STRUCTURE OF INVASIN: A BACTERIAL INTEGRIN-BINDING PROTEIN Deposited 1999-08-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 495–986（492 aa） Fragment：C-TERMINAL EXTRACELLULAR FRAGMENT
Not recorded CIT CITRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；PEG 4000, SODIUM CITRATE, ISOPROPANOL, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.30 Å R-free 0.274

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

View Construct and Data Evidence
UniProt name INVA_YERPS
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–245； UniProt 147–390

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 4e1t

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4e1t
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4e1t
Deposition date deposition_date2012-03-07
Structure title titleX-ray crystal structure of the transmembrane beta-domain from invasin from Yersinia pseudotuberculosis
Keywords keywordsouter membrane beta barrel, adhesin, integrin, CELL ADHESION; CELL ADHESION
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier19.25 Å
Radius of gyration Rg (electron density) rg_electron18.61 Å
Forward intensity I(0) i014604400.00
Molecular weight molecular_weight31697.0 kDa
Excluded volume excluded_volume40960 ų
Envelope volume envelope_volume46575 ų
Hydration-shell volume shell_volume20680 ų
Envelope diameter envelope_diameter65.4 Å
Shell Rg shell_rg25.40 Å
Envelope Rg envelope_rg18.78 Å
Shape Rg shape_rg18.60 Å
Total Rg total_rg19.73 Å
Total atoms total_atoms2243
Residues n_residues245
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax63.9 Å
Rg (real space) rg_real19.23 Å
Rg uncertainty (real space) rg_real_error0.38 Å
I(0) (real space) i0_real1.4600e+07
I(0) uncertainty (real space) i0_real_error1.8480e+05
Rg (reciprocal space) rg_reciprocal19.23 Å
I(0) (reciprocal space) i0_reciprocal14600000.0000
Solution quality estimate total_estimate0.8796
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.1 Å
Skewness Skewness skewness0.338
Kurtosis Kurtosis kurtosis-0.302
Angular range angular_range— – 0.4150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3165000.0000
Real-space data points n_real_points73
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.830; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.951
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id4e1tA00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology160 — Porin
Homologous superfamily homologous superfamily160 — Inverse autotransporter, beta-domain
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8. Citations (1)

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9. Files and Curves (10)