1ba3

FIREFLY LUCIFERASE IN COMPLEX WITH BROMOFORM

Method: X-RAY DIFFRACTION Dmax: 84.2 Å Quality: GOOD

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

LUCIFERASE

Photinus pyralis

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 MBR TRIBROMOMETHANE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:microbatch under oil;pH 7.8;283 K;2 MICROLITRE OF LUCIFERASE (20 MG/ML) IN 0.2M AMMONIUM SULFATE, 0.001M EDTA, 0.001M DTT, 10% GLYCEROL, 25% ETHYLENE GLYCOL, 0.025M TRIS-HCL PH7.8 + 2 MICROLITRE 0.5M LITHIUM SULFATE, 26% PEG 8000, 0.1M TRIS-HCL PH7.8 AT 10 DEGREES CELSIUS IN MICROBATCH UNDER OIL., microbatch under oil, temperature 283K Resolution 2.20 Å R-free 0.239

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 1ba3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1ba3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1ba3
Deposition date deposition_date1998-04-21
Structure title titleFIREFLY LUCIFERASE IN COMPLEX WITH BROMOFORM
Keywords keywordsOXIDOREDUCTASE, MONOOXYGENASE, PHOTOPROTEIN, LUMINESCENCE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier25.35
Radius of gyration Rg (electron density) rg_electron24.51
Forward intensity I(0) i054438500.00
Molecular weight molecular_weight59026.0 kDa
Excluded volume excluded_volume74403 ų
Envelope volume envelope_volume88240 ų
Hydration-shell volume shell_volume29876 ų
Envelope diameter envelope_diameter88.2
Shell Rg shell_rg31.85
Envelope Rg envelope_rg24.54
Shape Rg shape_rg24.55
Total Rg total_rg25.17
Total atoms total_atoms4138
Residues n_residues540
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 dmax84.2
Rg (real space) rg_real25.28
Rg uncertainty (real space) rg_real_error0.65
I(0) (real space) i0_real5.4440e+07
I(0) uncertainty (real space) i0_real_error7.0330e+05
Rg (reciprocal space) rg_reciprocal25.30
I(0) (reciprocal space) i0_reciprocal54440000.0000
Solution quality estimate total_estimate0.8872
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.7
Skewness Skewness skewness0.270
Kurtosis Kurtosis kurtosis-0.327
Angular range angular_range— – 0.3150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11250000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.851; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.990

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1ba3a_
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 (3 domains)

Domain ID domain_id1ba3A01
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology38 — Luciferase; domain 3
Homologous superfamily homologous superfamily10 — Luciferase; Domain 3
Domain ID domain_id1ba3A02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily980
Domain ID domain_id1ba3A03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily980

8. Citations (4)

9. Files and Curves (10)