6cbv

Crystal structure of BRIL bound to an affinity matured synthetic antibody.

Method: X-RAY DIFFRACTION Dmax: 95.2 Å Quality: GOOD

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

BRIL

Escherichia coli

UniProt P0ABE7

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 23–128 Mutation:M7W, H102I, R106L Heavy chain, Fab fragment × 1 Light Chain, Fab fragment × 1 GOL GLYCEROL × 2 FMT FORMIC ACID × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;0.2 M Sodium formate, 20 % w/v PEG 3350 Resolution 1.87 Å R-free 0.225

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.

714 other PDB entries and 822 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name C562_ECOLX
Isoform
PDB entities 3
Chains and sequence ranges Author chain B; PDBConstruct 1–106; UniProt 23–128

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 6cbv

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6cbv
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6cbv
Deposition date deposition_date2018-02-05
Structure title titleCrystal structure of BRIL bound to an affinity matured synthetic antibody.
Keywords keywords4-helix bundle, fusion protein, synthetic antibody, Fab fragment, fusion protein in complex with Fab, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier28.71
Radius of gyration Rg (electron density) rg_electron28.21
Forward intensity I(0) i057339700.00
Molecular weight molecular_weight58918.0 kDa
Excluded volume excluded_volume73482 ų
Envelope volume envelope_volume92906 ų
Hydration-shell volume shell_volume28813 ų
Envelope diameter envelope_diameter100.6
Shell Rg shell_rg34.11
Envelope Rg envelope_rg28.39
Shape Rg shape_rg28.17
Total Rg total_rg28.90
Total atoms total_atoms4150
Residues n_residues543
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 dmax95.2
Rg (real space) rg_real28.86
Rg uncertainty (real space) rg_real_error0.78
I(0) (real space) i0_real5.7340e+07
I(0) uncertainty (real space) i0_real_error9.1610e+05
Rg (reciprocal space) rg_reciprocal28.80
I(0) (reciprocal space) i0_reciprocal57340000.0000
Solution quality estimate total_estimate0.8627
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.2
Skewness Skewness skewness0.520
Kurtosis Kurtosis kurtosis-0.220
Angular range angular_range— – 0.2750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8747000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.839; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.882; Smooth: 0.813

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd6cbvb_
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.3 — Cytochromes
Family Family familya.24.3.1 — Cytochrome b562
Domain ID domain_idd6cbvh_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd6cbvl1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd6cbvl2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (3 domains)

Domain ID domain_id6cbvH02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6cbvL01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6cbvL02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)