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7fdy

Structure of OmpF1

Method: X-RAY DIFFRACTION Dmax: 87.6 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Porin OmpF

Escherichia coli

UniProt A0A418U3R0

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 10–349 Chain B； UniProt 10–349 Chain C； UniProt 10–349 Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；0.1 mM sodium cacodylate (pH 8.0), 43% PEG 200, 0.12 M MgCl2 Resolution 3.10 Å R-free 0.295

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 7FDY Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3O0E Crystal structure of OmpF in complex with colicin peptide OBS1 Deposited 2010-07-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 10–349（340 aa）
Chain C 10–349（340 aa）
Chain E 10–349（340 aa）
Not recorded BOG octyl beta-D-glucopyranoside × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；25% PEG 3350, 0.2M Li2SO4, 0.1M sodium cacodylate, pH 6.5, sitting drop vapor diffusion, temperature 293K
Resolution 3.01 Å R-free 0.302
3O0E Crystal structure of OmpF in complex with colicin peptide OBS1 Deposited 2010-07-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 10–349（340 aa）
Chain D 10–349（340 aa）
Chain F 10–349（340 aa）
Not recorded BOG octyl beta-D-glucopyranoside × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；25% PEG 3350, 0.2M Li2SO4, 0.1M sodium cacodylate, pH 6.5, sitting drop vapor diffusion, temperature 293K
Resolution 3.01 Å R-free 0.302

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A418U3R0_ECOLX
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–341； UniProt 10–349 Author chain B； PDBConstruct 2–341； UniProt 10–349 Author chain C； PDBConstruct 2–341； UniProt 10–349

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 7fdy

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7fdy
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7fdy
Deposition date deposition_date2021-07-18
Structure title titleStructure of OmpF1
Keywords keywordsMembrane protein; MEMBRANE PROTEIN
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_guinier30.74 Å
Radius of gyration Rg (electron density) rg_electron30.20 Å
Forward intensity I(0) i0200541000.00
Molecular weight molecular_weight106830.0 kDa
Excluded volume excluded_volume130700 ų
Envelope volume envelope_volume174430 ų
Hydration-shell volume shell_volume46441 ų
Envelope diameter envelope_diameter92.8 Å
Shell Rg shell_rg38.91 Å
Envelope Rg envelope_rg29.79 Å
Shape Rg shape_rg30.22 Å
Total Rg total_rg30.90 Å
Total atoms total_atoms7572
Residues n_residues1014
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 dmax87.6 Å
Rg (real space) rg_real30.52 Å
Rg uncertainty (real space) rg_real_error0.35 Å
I(0) (real space) i0_real2.0050e+08
I(0) uncertainty (real space) i0_real_error2.9070e+06
Rg (reciprocal space) rg_reciprocal30.62 Å
I(0) (reciprocal space) i0_reciprocal200600000.0000
Solution quality estimate total_estimate0.9080
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary37.1 Å
Skewness Skewness skewness0.052
Kurtosis Kurtosis kurtosis-0.639
Angular range angular_range— – 0.2600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha16880000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.982; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.872
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)