3ier

Firefly luciferase apo structure (P41 form) with PEG 400 bound

Method: X-RAY DIFFRACTION Dmax: 71.8 Å Quality: GOOD

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

Luciferin 4-monooxygenase

OrganismNot specified

UniProt P08659

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 1–550 Not recorded PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 8.5;277 K;25% PEG 400, 20% PEG 3350, 0.1M MgCl2, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, temperature 277K Resolution 2.05 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.

17 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LUCI_PHOPY
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–550; UniProt 1–550

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 3ier

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3ier
Deposition date deposition_date2009-07-23
Structure title titleFirefly luciferase apo structure (P41 form) with PEG 400 bound
Keywords keywordsOXIDOREDUCTASE, MONOOXYGENASE, PHOTOPROTEIN, LUMINESCENCE, ATP-binding, Magnesium, Metal-binding, Nucleotide-binding, Peroxisome; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier22.60
Radius of gyration Rg (electron density) rg_electron21.44
Forward intensity I(0) i034913900.00
Molecular weight molecular_weight47477.0 kDa
Excluded volume excluded_volume60196 ų
Envelope volume envelope_volume67807 ų
Hydration-shell volume shell_volume25808 ų
Envelope diameter envelope_diameter71.6
Shell Rg shell_rg28.85
Envelope Rg envelope_rg21.64
Shape Rg shape_rg21.44
Total Rg total_rg22.34
Total atoms total_atoms3349
Residues n_residues427
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 dmax71.8
Rg (real space) rg_real22.49
Rg uncertainty (real space) rg_real_error0.32
I(0) (real space) i0_real3.4910e+07
I(0) uncertainty (real space) i0_real_error4.4570e+05
Rg (reciprocal space) rg_reciprocal22.52
I(0) (reciprocal space) i0_reciprocal34910000.0000
Solution quality estimate total_estimate0.8995
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.3
Skewness Skewness skewness0.175
Kurtosis Kurtosis kurtosis-0.466
Angular range angular_range— – 0.3500 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha8322000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.998

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3iera_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.23 — Acetyl-CoA synthetase-like
Superfamily Superfamily superfamilye.23.1 — Acetyl-CoA synthetase-like
Family Family familye.23.1.1 — Acetyl-CoA synthetase-like

CATH v4.4 (1 domains)

Domain ID domain_id3ierA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily12780 — ANL, N-terminal domain

8. Citations (1)

9. Files and Curves (10)