1n2z

2.0 Angstrom structure of BtuF, the vitamin B12 binding protein of E. coli

Method: X-RAY DIFFRACTION Dmax: 94.9 Å Quality: REASONABLE

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

Vitamin B12 transport protein btuF

Escherichia coli

UniProt P37028

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 22–266 Not recorded CD CADMIUM ION × 13 CL CHLORIDE ION × 4 CNC CYANOCOBALAMIN × 1 PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.00 Å R-free 0.210
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 22–266 Not recorded CD CADMIUM ION × 9 CL CHLORIDE ION × 2 CNC CYANOCOBALAMIN × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.00 Å R-free 0.210
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 22–266 Chain B; UniProt 22–266 Not recorded CD CADMIUM ION × 22 CL CHLORIDE ION × 6 CNC CYANOCOBALAMIN × 2 PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.00 Å R-free 0.210
4 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 22–266 Chain B; UniProt 22–266 Not recorded CD CADMIUM ION × 22 CL CHLORIDE ION × 6 CNC CYANOCOBALAMIN × 2 PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.00 Å R-free 0.210

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.

10 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BTUF_ECOLI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–245; UniProt 22–266 Author chain B; PDBConstruct 1–245; UniProt 22–266

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 1n2z

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1n2z
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1n2z
Deposition date deposition_date2002-10-24
Structure title title2.0 Angstrom structure of BtuF, the vitamin B12 binding protein of E. coli
Keywords keywordsTRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier24.73
Radius of gyration Rg (electron density) rg_electron23.89
Forward intensity I(0) i063594900.00
Molecular weight molecular_weight59589.0 kDa
Excluded volume excluded_volume72923 ų
Envelope volume envelope_volume86387 ų
Hydration-shell volume shell_volume29700 ų
Envelope diameter envelope_diameter78.4
Shell Rg shell_rg31.47
Envelope Rg envelope_rg24.04
Shape Rg shape_rg23.87
Total Rg total_rg24.75
Total atoms total_atoms4039
Residues n_residues490
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 dmax94.9
Rg (real space) rg_real24.62
Rg uncertainty (real space) rg_real_error0.78
I(0) (real space) i0_real6.3590e+07
I(0) uncertainty (real space) i0_real_error1.0240e+06
Rg (reciprocal space) rg_reciprocal24.65
I(0) (reciprocal space) i0_reciprocal63600000.0000
Solution quality estimate total_estimate0.7287
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary28.6
Skewness Skewness skewness0.246
Kurtosis Kurtosis kurtosis-0.430
Angular range angular_range— – 0.3200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha19950000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.542; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.844; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1n2za_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.92 — Chelatase-like
Superfamily Superfamily superfamilyc.92.2 — 'Helical backbone' metal receptor
Family Family familyc.92.2.2 — TroA-like
Domain ID domain_idd1n2zb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.92 — Chelatase-like
Superfamily Superfamily superfamilyc.92.2 — 'Helical backbone' metal receptor
Family Family familyc.92.2.2 — TroA-like

CATH v4.4 (4 domains)

Domain ID domain_id1n2zA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1980 — Nitrogenase molybdenum iron protein domain
Domain ID domain_id1n2zA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1980 — Nitrogenase molybdenum iron protein domain
Domain ID domain_id1n2zB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1980 — Nitrogenase molybdenum iron protein domain
Domain ID domain_id1n2zB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1980 — Nitrogenase molybdenum iron protein domain

8. Citations (1)

9. Files and Curves (10)