4dql

Crystal structure of the FAD binding domain of cytochrome P450 BM3 in complex with NADP+

Method: X-RAY DIFFRACTION Dmax: 151.3 Å Quality: REASONABLE

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

Bifunctional P-450/NADPH-P450 reductase

Bacillus megaterium

UniProt P14779

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 657–1049 Fragment:Cytochrome P450 BM3,UNP residues 657-1049 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 SO4 SULFATE ION × 1 1PE PENTAETHYLENE GLYCOL × 1 PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;293 K;Sitting drops were prepared by adding 2 l of mother liquor to 2 l of 12 mg/ml FAD domain. Crystals were obtained using a well solution of 28% polyethylene glycol 8000, 0.3 M ammonium sulfate, cacodylate buffer pH 6.5. Crystals of dimensions 70 x 70 x 900 M formed after 4-7 days. In order to form a coenzyme complex with NADP+, C773A/C999A FAD domain crystals were soaked in a 10 mM NADP+ solution for 10 minutes., VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.15 Å R-free 0.226
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 657–1049 Fragment:Cytochrome P450 BM3,UNP residues 657-1049 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 SO4 SULFATE ION × 1 PG4 TETRAETHYLENE GLYCOL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;293 K;Sitting drops were prepared by adding 2 l of mother liquor to 2 l of 12 mg/ml FAD domain. Crystals were obtained using a well solution of 28% polyethylene glycol 8000, 0.3 M ammonium sulfate, cacodylate buffer pH 6.5. Crystals of dimensions 70 x 70 x 900 M formed after 4-7 days. In order to form a coenzyme complex with NADP+, C773A/C999A FAD domain crystals were soaked in a 10 mM NADP+ solution for 10 minutes., VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.15 Å R-free 0.226
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 657–1049 Chain B; UniProt 657–1049 Fragment:Cytochrome P450 BM3,UNP residues 657-1049 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 SO4 SULFATE ION × 2 1PE PENTAETHYLENE GLYCOL × 1 PG4 TETRAETHYLENE GLYCOL × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;293 K;Sitting drops were prepared by adding 2 l of mother liquor to 2 l of 12 mg/ml FAD domain. Crystals were obtained using a well solution of 28% polyethylene glycol 8000, 0.3 M ammonium sulfate, cacodylate buffer pH 6.5. Crystals of dimensions 70 x 70 x 900 M formed after 4-7 days. In order to form a coenzyme complex with NADP+, C773A/C999A FAD domain crystals were soaked in a 10 mM NADP+ solution for 10 minutes., VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.15 Å R-free 0.226

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.

168 other PDB entries and 309 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CPXB_BACME
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–393; UniProt 657–1049 Author chain B; PDBConstruct 1–393; UniProt 657–1049

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 4dql

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4dql
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id4dql
Deposition date deposition_date2012-02-16
Structure title titleCrystal structure of the FAD binding domain of cytochrome P450 BM3 in complex with NADP+
Keywords keywordsRossmann fold, redox, FAD and NADP+ binding, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier46.95
Radius of gyration Rg (electron density) rg_electron47.76
Forward intensity I(0) i0117586000.00
Molecular weight molecular_weight87027.0 kDa
Excluded volume excluded_volume107860 ų
Envelope volume envelope_volume160910 ų
Hydration-shell volume shell_volume28938 ų
Envelope diameter envelope_diameter162.1
Shell Rg shell_rg50.02
Envelope Rg envelope_rg46.40
Shape Rg shape_rg47.76
Total Rg total_rg47.86
Total atoms total_atoms6113
Residues n_residues757
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 dmax151.3
Rg (real space) rg_real47.67
Rg uncertainty (real space) rg_real_error2.02
I(0) (real space) i0_real1.1760e+08
I(0) uncertainty (real space) i0_real_error2.1470e+06
Rg (reciprocal space) rg_reciprocal46.95
I(0) (reciprocal space) i0_reciprocal117500000.0000
Solution quality estimate total_estimate0.6279
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.7
Skewness Skewness skewness0.371
Kurtosis Kurtosis kurtosis-0.918
Angular range angular_range— – 0.1700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4379000.0000
Real-space data points n_real_points35
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.285; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.266; Smooth: 0.039

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd4dqla1
Class classb — All beta proteins
Fold Fold foldb.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamilyb.43.4 — Riboflavin synthase domain-like
Family Family familyb.43.4.0 — automated matches
Domain ID domain_idd4dqla2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.25 — Ferredoxin reductase-like, C-terminal NADP-linked domain
Superfamily Superfamily superfamilyc.25.1 — Ferredoxin reductase-like, C-terminal NADP-linked domain
Family Family familyc.25.1.0 — automated matches
Domain ID domain_idd4dqlb1
Class classb — All beta proteins
Fold Fold foldb.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamilyb.43.4 — Riboflavin synthase domain-like
Family Family familyb.43.4.0 — automated matches
Domain ID domain_idd4dqlb2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.25 — Ferredoxin reductase-like, C-terminal NADP-linked domain
Superfamily Superfamily superfamilyc.25.1 — Ferredoxin reductase-like, C-terminal NADP-linked domain
Family Family familyc.25.1.0 — automated matches

CATH v4.4 (6 domains)

Domain ID domain_id4dqlA01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily10 — Translation factors
Domain ID domain_id4dqlA02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology990 — NADPH-cytochrome p450 Reductase; Chain A, domain 3
Homologous superfamily homologous superfamily10 — NADPH-cytochrome p450 Reductase; Chain A, domain 3
Domain ID domain_id4dqlA03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily80 — Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module
Domain ID domain_id4dqlB01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily10 — Translation factors
Domain ID domain_id4dqlB02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology990 — NADPH-cytochrome p450 Reductase; Chain A, domain 3
Homologous superfamily homologous superfamily10 — NADPH-cytochrome p450 Reductase; Chain A, domain 3
Domain ID domain_id4dqlB03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily80 — Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module

8. Citations (1)

9. Files and Curves (10)