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3rfj

Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering

Method: X-RAY DIFFRACTION Dmax: 81.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Internalin B, repeat modules, Variable lymphocyte receptor

synthetic

UniProt D2P9A6

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 36–100 Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8；293 K；25.5% polyethylene glycol 4000, 15%(w/v) glycerol, 0.17M ammonium sulfate, pH 8.0, VAPOR DIFFUSION, temperature 293K Resolution 1.78 Å R-free 0.260

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.

Other PDB Difference from Current Entry 3RFJ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3RFS Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering Deposited 2011-04-06 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–100（65 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；0.1M Tris-HCl, 30%(w/v) polyethylene glycol 4000, 0.2M magnesium chloride hexahydrate, pH 8.5, VAPOR DIFFUSION, temperature 293K
Resolution 1.70 Å R-free 0.242
3RFS Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering Deposited 2011-04-06 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 36–100（65 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；0.1M Tris-HCl, 30%(w/v) polyethylene glycol 4000, 0.2M magnesium chloride hexahydrate, pH 8.5, VAPOR DIFFUSION, temperature 293K
Resolution 1.70 Å R-free 0.242

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name D2P9A6_LISM2
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–65； UniProt 36–100

Internalin B, repeat modules, Variable lymphocyte receptor

synthetic

UniProt Q6E4K6

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 130–189 Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8；293 K；25.5% polyethylene glycol 4000, 15%(w/v) glycerol, 0.17M ammonium sulfate, pH 8.0, VAPOR DIFFUSION, temperature 293K Resolution 1.78 Å R-free 0.260

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name Q6E4K6_PETMA
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 214–273； UniProt 130–189

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 3rfj

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3rfj
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3rfj
Deposition date deposition_date2011-04-06
Structure title titleDesign of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering
Keywords keywordsLRR, protein binding, plasma; PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier22.78 Å
Radius of gyration Rg (electron density) rg_electron21.84 Å
Forward intensity I(0) i015600200.00
Molecular weight molecular_weight30045.0 kDa
Excluded volume excluded_volume37777 ų
Envelope volume envelope_volume44596 ų
Hydration-shell volume shell_volume18518 ų
Envelope diameter envelope_diameter84.0 Å
Shell Rg shell_rg27.21 Å
Envelope Rg envelope_rg22.23 Å
Shape Rg shape_rg21.78 Å
Total Rg total_rg22.80 Å
Total atoms total_atoms2115
Residues n_residues268
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax81.4 Å
Rg (real space) rg_real22.97 Å
Rg uncertainty (real space) rg_real_error0.63 Å
I(0) (real space) i0_real1.5600e+07
I(0) uncertainty (real space) i0_real_error2.0970e+05
Rg (reciprocal space) rg_reciprocal22.93 Å
I(0) (reciprocal space) i0_reciprocal15600000.0000
Solution quality estimate total_estimate0.8216
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.4 Å
Skewness Skewness skewness0.607
Kurtosis Kurtosis kurtosis-0.007
Angular range angular_range— – 0.3500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2048000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.616; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.836; Smooth: 0.993
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id3rfjA00
Class class3 — Alpha Beta
Architecture architecture80 — Alpha-Beta Horseshoe
Topology topology10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily10 — Ribonuclease Inhibitor
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8. Citations (1)

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9. Files and Curves (10)