1n4a

The Ligand Bound Structure of E.coli BtuF, the Periplasmic Binding Protein for Vitamin B12

Method: X-RAY DIFFRACTION Dmax: 75.2 Å Quality: EXCELLENT

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 23–266 Non-standard monomer:Yes (specific site not provided by mmCIF) CNC CYANOCOBALAMIN × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.6;294 K;NaCl, ethanol, acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K Resolution 2.00 Å R-free 0.261
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 23–266 Non-standard monomer:Yes (specific site not provided by mmCIF) CNC CYANOCOBALAMIN × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.6;294 K;NaCl, ethanol, acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K Resolution 2.00 Å R-free 0.261

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 24 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 1–244; UniProt 23–266 Author chain B; PDBConstruct 1–244; UniProt 23–266

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 1n4a

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1n4a
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1n4a
Deposition date deposition_date2002-10-30
Structure title titleThe Ligand Bound Structure of E.coli BtuF, the Periplasmic Binding Protein for Vitamin B12
Keywords keywords;ABC transporter, periplasmic binding protein, Vitamin B12, transmembrane transport, Structural Genomics, PSI, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, TRANSPORT PROTEIN ;; TRANSPORT PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier24.30
Radius of gyration Rg (electron density) rg_electron23.41
Forward intensity I(0) i051611300.00
Molecular weight molecular_weight56776.0 kDa
Excluded volume excluded_volume71457 ų
Envelope volume envelope_volume83901 ų
Hydration-shell volume shell_volume29311 ų
Envelope diameter envelope_diameter76.8
Shell Rg shell_rg31.07
Envelope Rg envelope_rg23.49
Shape Rg shape_rg23.41
Total Rg total_rg24.26
Total atoms total_atoms3990
Residues n_residues484
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 dmax75.2
Rg (real space) rg_real24.16
Rg uncertainty (real space) rg_real_error0.41
I(0) (real space) i0_real5.1610e+07
I(0) uncertainty (real space) i0_real_error6.6180e+05
Rg (reciprocal space) rg_reciprocal24.19
I(0) (reciprocal space) i0_reciprocal51610000.0000
Solution quality estimate total_estimate0.9055
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.9
Skewness Skewness skewness0.180
Kurtosis Kurtosis kurtosis-0.488
Angular range angular_range— – 0.3250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha16830000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.983

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1n4aa_
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_idd1n4ab_
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_id1n4aA01
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_id1n4aA02
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_id1n4aB01
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_id1n4aB02
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)