1ujw

Structure of the complex between BtuB and Colicin E3 Receptor binding domain

Method: X-RAY DIFFRACTION Dmax: 89.8 Å Quality: REASONABLE

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

Vitamin B12 receptor

Escherichia coli

UniProt P06129

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 21–614 Not recorded Colicin E3 × 1 (P00646) GP1 2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose × 2 LIM 3-OXO-PENTADECANOIC ACID × 2 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 7 AAE ACETOACETIC ACID × 1 GOL GLYCEROL × 8 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.75 Å R-free 0.293

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.

12 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BTUB_ECOLI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–594; UniProt 21–614

Colicin E3

Escherichia coli

UniProt P00646

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 314–448 Fragment:R-domain(residues 314-448) Vitamin B12 receptor × 1 (P06129) GP1 2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose × 2 LIM 3-OXO-PENTADECANOIC ACID × 2 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 7 AAE ACETOACETIC ACID × 1 GOL GLYCEROL × 8 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.75 Å R-free 0.293

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.

5 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CEA3_ECOLI
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–135; UniProt 314–448

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 1ujw

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1ujw
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id1ujw
Deposition date deposition_date2003-08-12
Structure title titleStructure of the complex between BtuB and Colicin E3 Receptor binding domain
Keywords keywordsbeta-barrel, coiled-coil, TRANSPORT PROTEIN-HYDROLASE COMPLEX; TRANSPORT PROTEIN/HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier30.96
Radius of gyration Rg (electron density) rg_electron31.34
Forward intensity I(0) i0106483000.00
Molecular weight molecular_weight80729.0 kDa
Excluded volume excluded_volume100590 ų
Envelope volume envelope_volume131070 ų
Hydration-shell volume shell_volume37615 ų
Envelope diameter envelope_diameter138.0
Shell Rg shell_rg35.36
Envelope Rg envelope_rg33.77
Shape Rg shape_rg31.31
Total Rg total_rg31.79
Total atoms total_atoms5704
Residues n_residues692
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 dmax89.8
Rg (real space) rg_real27.99
Rg uncertainty (real space) rg_real_error0.30
I(0) (real space) i0_real1.0100e+08
I(0) uncertainty (real space) i0_real_error1.3740e+06
Rg (reciprocal space) rg_reciprocal31.40
I(0) (reciprocal space) i0_reciprocal106500000.0000
Solution quality estimate total_estimate0.6397
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.4
Skewness Skewness skewness0.583
Kurtosis Kurtosis kurtosis0.323
Angular range angular_range— – 0.2550 −1
Current regularization parameter α current_alpha0.7136
Highest regularization parameter α highest_alpha13050000.0000
Real-space data points n_real_points52
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.001; Oscil: 0.770; Stabil: 0.985; Sysdev: 0.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.131

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1ujwa_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.4 — Transmembrane beta-barrels
Superfamily Superfamily superfamilyf.4.3 — Porins
Family Family familyf.4.3.3 — Ligand-gated protein channel
Domain ID domain_idd1ujwb_
Class classh — Coiled coil proteins
Fold Fold foldh.4 — Antiparallel coiled-coil
Superfamily Superfamily superfamilyh.4.9 — Colicin E3 receptor domain
Family Family familyh.4.9.1 — Colicin E3 receptor domain

CATH v4.4 (3 domains)

Domain ID domain_id1ujwA01
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology130 — Ferric Hydroxamate Uptake Protein; Chain A, domain 1
Homologous superfamily homologous superfamily10 — TonB-dependent receptor, plug domain
Domain ID domain_id1ujwA02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology170 — Maltoporin; Chain A
Homologous superfamily homologous superfamily20 — TonB-dependent receptor, beta-barrel domain
Domain ID domain_id1ujwB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily620 — Helix Hairpins

8. Citations (1)

9. Files and Curves (10)