3wsp

Crystal Structure of P450BM3 with N-perfluorononanoyl-L-tryptophan

Method: X-RAY DIFFRACTION Dmax: 112.6 Å Quality: GOOD

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 1–456 Fragment:UNP Residues 1-455 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 W09 N-(2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,9-heptadecafluorononanoyl)-L-tryptophan × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.9;293 K;75mM Tris-HCl (pH7.9), 50uM N-perfluorononanoyl L-tryptophan, 0.5% (v/v) dimethyl sulfoxide, 105mM MgCl and 10.5% (w/v) PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 1.80 Å R-free 0.212
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1–456 Fragment:UNP Residues 1-455 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 W09 N-(2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,9-heptadecafluorononanoyl)-L-tryptophan × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.9;293 K;75mM Tris-HCl (pH7.9), 50uM N-perfluorononanoyl L-tryptophan, 0.5% (v/v) dimethyl sulfoxide, 105mM MgCl and 10.5% (w/v) PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 1.80 Å R-free 0.212

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 310 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 1–456; UniProt 1–456 Author chain B; PDBConstruct 1–456; UniProt 1–456

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 3wsp

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3wsp
Deposition date deposition_date2014-03-20
Structure title titleCrystal Structure of P450BM3 with N-perfluorononanoyl-L-tryptophan
Keywords keywordsCytochrome P450, Oxidoreductase; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier34.08
Radius of gyration Rg (electron density) rg_electron33.58
Forward intensity I(0) i0170596000.00
Molecular weight molecular_weight106400.0 kDa
Excluded volume excluded_volume133520 ų
Envelope volume envelope_volume163220 ų
Hydration-shell volume shell_volume40994 ų
Envelope diameter envelope_diameter119.8
Shell Rg shell_rg39.72
Envelope Rg envelope_rg33.52
Shape Rg shape_rg33.58
Total Rg total_rg34.00
Total atoms total_atoms7488
Residues n_residues906
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 dmax112.6
Rg (real space) rg_real34.20
Rg uncertainty (real space) rg_real_error0.78
I(0) (real space) i0_real1.7060e+08
I(0) uncertainty (real space) i0_real_error2.7100e+06
Rg (reciprocal space) rg_reciprocal34.13
I(0) (reciprocal space) i0_reciprocal170600000.0000
Solution quality estimate total_estimate0.8747
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.3
Skewness Skewness skewness0.441
Kurtosis Kurtosis kurtosis-0.409
Angular range angular_range— – 0.2300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha43900000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.840; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.877

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3wspa_
Class classa — All alpha proteins
Fold Fold folda.104 — Cytochrome P450
Superfamily Superfamily superfamilya.104.1 — Cytochrome P450
Family Family familya.104.1.1 — Cytochrome P450
Domain ID domain_idd3wspb_
Class classa — All alpha proteins
Fold Fold folda.104 — Cytochrome P450
Superfamily Superfamily superfamilya.104.1 — Cytochrome P450
Family Family familya.104.1.1 — Cytochrome P450

CATH v4.4 (2 domains)

Domain ID domain_id3wspA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450
Domain ID domain_id3wspB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450

8. Citations (1)

9. Files and Curves (10)