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1xkj

BACTERIAL LUCIFERASE BETA2 HOMODIMER

Method: X-RAY DIFFRACTION Dmax: 83.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

BETA2 LUCIFERASE

Vibrio harveyi

UniProt P07739

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–324 Chain B； UniProt 1–324 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.2；277 K；SITTING DROP, 277 KELVIN, 12% PEG 4000, 17-21% ISOPROPANOL, 0.006M DTT, 0.1M CITRATE PH 6.2. 50 MG/ML PROTEIN., vapor diffusion - sitting drop Resolution 2.50 Å R-free 0.249

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 1XKJ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BRL THREE-DIMENSIONAL STRUCTURE OF BACTERIAL LUCIFERASE FROM VIBRIO HARVEYI AT 2.4 ANGSTROMS RESOLUTION Deposited 1995-03-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–324（324 aa）
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å
1BRL THREE-DIMENSIONAL STRUCTURE OF BACTERIAL LUCIFERASE FROM VIBRIO HARVEYI AT 2.4 ANGSTROMS RESOLUTION Deposited 1995-03-20 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–324（324 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å
1BSL STRUCTURE OF ALKANAL MONOOXYGENASE BETA CHAIN Deposited 1996-10-22 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–324（324 aa） Fragment：BETA SUBUNIT
Chain B 1–324（324 aa） Fragment：BETA SUBUNIT
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.95 Å
1LUC BACTERIAL LUCIFERASE Deposited 1996-05-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–324（324 aa）
Not recorded MG MAGNESIUM ION × 3 EDO 1,2-ETHANEDIOL × 5 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.50 Å
3FGC Crystal Structure of the Bacterial Luciferase:Flavin Complex Reveals the Basis of Intersubunit Communication Deposited 2008-12-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–324（324 aa）
Not recorded FMN FLAVIN MONONUCLEOTIDE × 1 PO4 PHOSPHATE ION × 1 SO4 SULFATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；100 mM Na+/K+ phosphate pH 7.5 and 1.65 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.30 Å R-free 0.241
3FGC Crystal Structure of the Bacterial Luciferase:Flavin Complex Reveals the Basis of Intersubunit Communication Deposited 2008-12-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–324（324 aa）
Not recorded PO4 PHOSPHATE ION × 1 SO4 SULFATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；100 mM Na+/K+ phosphate pH 7.5 and 1.65 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.30 Å R-free 0.241

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LUXB_VIBHA
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–324； UniProt 1–324 Author chain B； PDBConstruct 1–324； UniProt 1–324

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 1xkj

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1xkj
Deposition date deposition_date1996-10-08
Structure title titleBACTERIAL LUCIFERASE BETA2 HOMODIMER
Keywords keywordsLUCIFERASE, LUMINESCENCE, PHOTOPROTEIN, OXIDOREDUCTASE; LUMINESCENCE
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_guinier27.22 Å
Radius of gyration Rg (electron density) rg_electron26.08 Å
Forward intensity I(0) i088348400.00
Molecular weight molecular_weight71847.0 kDa
Excluded volume excluded_volume88945 ų
Envelope volume envelope_volume108590 ų
Hydration-shell volume shell_volume34296 ų
Envelope diameter envelope_diameter86.3 Å
Shell Rg shell_rg34.18 Å
Envelope Rg envelope_rg26.21 Å
Shape Rg shape_rg26.07 Å
Total Rg total_rg26.94 Å
Total atoms total_atoms5061
Residues n_residues648
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 dmax83.6 Å
Rg (real space) rg_real27.18 Å
Rg uncertainty (real space) rg_real_error0.59 Å
I(0) (real space) i0_real8.8350e+07
I(0) uncertainty (real space) i0_real_error1.3070e+06
Rg (reciprocal space) rg_reciprocal27.20 Å
I(0) (reciprocal space) i0_reciprocal88350000.0000
Solution quality estimate total_estimate0.8897
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.3 Å
Skewness Skewness skewness0.348
Kurtosis Kurtosis kurtosis-0.353
Angular range angular_range— – 0.2900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha22830000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.797
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1xkja_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.16 — Bacterial luciferase-like
Family Family familyc.1.16.1 — Bacterial luciferase (alkanal monooxygenase)
Domain ID domain_idd1xkjb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.16 — Bacterial luciferase-like
Family Family familyc.1.16.1 — Bacterial luciferase (alkanal monooxygenase)

CATH v4.4 (2 domains)

Domain ID domain_id1xkjA00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily30 — Luciferase-like domain
Domain ID domain_id1xkjB00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily30 — Luciferase-like domain
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8. Citations (1)

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9. Files and Curves (10)