4wf0

Crystal Structure of iLID - an Improved Light-Inducible Dimer

Method: X-RAY DIFFRACTION Dmax: 73.5 Å Quality: GOOD

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

NPH1-1

Avena sativa

UniProt O49003

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 404–543 Fragment:UNP residues 405-543 FMN FLAVIN MONONUCLEOTIDE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;298 K;Grown in dark for 3 days. Conditions: 100mM TRIS:HCl pH 8.5, 800mM Lithium Chloride, 32% PEG 4000 Resolution 1.95 Å R-free 0.244
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 404–543 Fragment:UNP residues 405-543 FMN FLAVIN MONONUCLEOTIDE × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;298 K;Grown in dark for 3 days. Conditions: 100mM TRIS:HCl pH 8.5, 800mM Lithium Chloride, 32% PEG 4000 Resolution 1.95 Å R-free 0.244

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.

17 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name O49003_AVESA
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 13–152; UniProt 404–543 Author chain B; PDBConstruct 13–152; UniProt 404–543

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 4wf0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4wf0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4wf0
Deposition date deposition_date2014-09-11
Structure title titleCrystal Structure of iLID - an Improved Light-Inducible Dimer
Keywords keywordslight-inducible dimer, FLAVOPROTEIN; FLAVOPROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier22.07
Radius of gyration Rg (electron density) rg_electron21.29
Forward intensity I(0) i021220900.00
Molecular weight molecular_weight34296.0 kDa
Excluded volume excluded_volume42648 ų
Envelope volume envelope_volume51529 ų
Hydration-shell volume shell_volume20643 ų
Envelope diameter envelope_diameter73.1
Shell Rg shell_rg27.39
Envelope Rg envelope_rg21.59
Shape Rg shape_rg21.27
Total Rg total_rg22.17
Total atoms total_atoms4771
Residues n_residues288
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 dmax73.5
Rg (real space) rg_real22.10
Rg uncertainty (real space) rg_real_error0.39
I(0) (real space) i0_real2.1220e+07
I(0) uncertainty (real space) i0_real_error2.8640e+05
Rg (reciprocal space) rg_reciprocal22.09
I(0) (reciprocal space) i0_reciprocal21220000.0000
Solution quality estimate total_estimate0.8801
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.1
Skewness Skewness skewness0.403
Kurtosis Kurtosis kurtosis-0.320
Angular range angular_range— – 0.3600 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha6505000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.829; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.955; Smooth: 0.996

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id4wf0A00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology450 — Beta-Lactamase
Homologous superfamily homologous superfamily20 — PAS domain
Domain ID domain_id4wf0B00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology450 — Beta-Lactamase
Homologous superfamily homologous superfamily20 — PAS domain

8. Citations (2)

9. Files and Curves (10)