7fbb

De novo design protein D12 with MBP tag

Method: X-RAY DIFFRACTION Dmax: 110.9 Å Quality: GOOD

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

Maltodextrin-binding protein,de novo designed protein D12

synthetic construct

UniProt A0A4P1LXE0

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 6–372 Mutation:D84A, K85A, E174A, N175A, K241A, E361A, K364A, D365A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;289 K;25% PEG 3350, 0.1M Sodium Acetate Resolution 2.31 Å R-free 0.264
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 6–372 Mutation:D84A, K85A, E174A, N175A, K241A, E361A, K364A, D365A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;289 K;25% PEG 3350, 0.1M Sodium Acetate Resolution 2.31 Å R-free 0.264

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.

28 other PDB entries and 46 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A4P1LXE0_SERSF
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–367; UniProt 6–372 Author chain B; PDBConstruct 1–367; UniProt 6–372

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 7fbb

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id7fbb
Deposition date deposition_date2021-07-09
Structure title titleDe novo design protein D12 with MBP tag
Keywords keywordsDE NOVO PROTEIN, UNKNOWN FUNCTION; UNKNOWN FUNCTION
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier32.35
Radius of gyration Rg (electron density) rg_electron31.63
Forward intensity I(0) i0131731000.00
Molecular weight molecular_weight94544.0 kDa
Excluded volume excluded_volume119730 ų
Envelope volume envelope_volume149380 ų
Hydration-shell volume shell_volume40030 ų
Envelope diameter envelope_diameter115.7
Shell Rg shell_rg37.90
Envelope Rg envelope_rg31.19
Shape Rg shape_rg31.59
Total Rg total_rg32.31
Total atoms total_atoms6680
Residues n_residues879
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 dmax110.9
Rg (real space) rg_real32.31
Rg uncertainty (real space) rg_real_error1.04
I(0) (real space) i0_real1.3170e+08
I(0) uncertainty (real space) i0_real_error2.2710e+06
Rg (reciprocal space) rg_reciprocal32.33
I(0) (reciprocal space) i0_reciprocal131700000.0000
Solution quality estimate total_estimate0.8745
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary40.7
Skewness Skewness skewness0.318
Kurtosis Kurtosis kurtosis-0.225
Angular range angular_range— – 0.2450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha30690000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.801; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.975

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id7fbbA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id7fbbB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II

8. Citations (1)

9. Files and Curves (10)