2qdf

Structure of N-terminal domain of E. Coli YaeT

Method: X-RAY DIFFRACTION Dmax: 85.6 Å Quality: GOOD

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

Outer membrane protein assembly factor yaeT

Escherichia coli K12

UniProt P0A940

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 21–351 Fragment:residues 21-351 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.8;295 K;10% PEG 10K, 100mM sodium acetate, 100 mM magnesium formate, 10%glycerol, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.20 Å R-free 0.286

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.

64 other PDB entries and 69 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name YAET_ECOLI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 5–335; UniProt 21–351

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 2qdf

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2qdf
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2qdf
Deposition date deposition_date2007-06-20
Structure title titleStructure of N-terminal domain of E. Coli YaeT
Keywords keywordsPOTRA domain, MEMBRANE PROTEIN, PROTEIN TRANSPORT; MEMBRANE PROTEIN, PROTEIN TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier28.02
Radius of gyration Rg (electron density) rg_electron27.21
Forward intensity I(0) i021259100.00
Molecular weight molecular_weight35401.0 kDa
Excluded volume excluded_volume44330 ų
Envelope volume envelope_volume63528 ų
Hydration-shell volume shell_volume20232 ų
Envelope diameter envelope_diameter85.2
Shell Rg shell_rg33.16
Envelope Rg envelope_rg26.21
Shape Rg shape_rg27.19
Total Rg total_rg27.95
Total atoms total_atoms2493
Residues n_residues318
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 dmax85.6
Rg (real space) rg_real27.95
Rg uncertainty (real space) rg_real_error0.61
I(0) (real space) i0_real2.1260e+07
I(0) uncertainty (real space) i0_real_error3.0150e+05
Rg (reciprocal space) rg_reciprocal27.98
I(0) (reciprocal space) i0_reciprocal21260000.0000
Solution quality estimate total_estimate0.8977
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary40.5
Skewness Skewness skewness0.063
Kurtosis Kurtosis kurtosis-0.760
Angular range angular_range— – 0.2850 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2820000.0000
Real-space data points n_real_points58
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.923; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.947; Smooth: 0.951

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd2qdfa1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.391 — POlypeptide TRansport Associated (PORTRA) domain-like
Superfamily Superfamily superfamilyd.391.1 — POlypeptide TRansport Associated (PORTRA) domain-like
Family Family familyd.391.1.1 — POlypeptide TRansport Associated (PORTRA) domain
Domain ID domain_idd2qdfa2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.391 — POlypeptide TRansport Associated (PORTRA) domain-like
Superfamily Superfamily superfamilyd.391.1 — POlypeptide TRansport Associated (PORTRA) domain-like
Family Family familyd.391.1.1 — POlypeptide TRansport Associated (PORTRA) domain
Domain ID domain_idd2qdfa3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.391 — POlypeptide TRansport Associated (PORTRA) domain-like
Superfamily Superfamily superfamilyd.391.1 — POlypeptide TRansport Associated (PORTRA) domain-like
Family Family familyd.391.1.1 — POlypeptide TRansport Associated (PORTRA) domain
Domain ID domain_idd2qdfa4
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.391 — POlypeptide TRansport Associated (PORTRA) domain-like
Superfamily Superfamily superfamilyd.391.1 — POlypeptide TRansport Associated (PORTRA) domain-like
Family Family familyd.391.1.1 — POlypeptide TRansport Associated (PORTRA) domain
Domain ID domain_idd2qdfa5
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id2qdfA01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily310 — membrane protein fhac
Domain ID domain_id2qdfA02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily310 — membrane protein fhac
Domain ID domain_id2qdfA03
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily310 — membrane protein fhac
Domain ID domain_id2qdfA04
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily310 — membrane protein fhac

8. Citations (1)

9. Files and Curves (10)