4hgf

Crystal structure of P450 BM3 5F5K heme domain variant complexed with styrene

Method: X-RAY DIFFRACTION Dmax: 116.6 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 2–456 Fragment:Heme-binding domain Mutation:F87A, A184K, T235A HEM PROTOPORPHYRIN IX CONTAINING FE × 1 SYN ethenylbenzene × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;277 K;300 mM magnesium formate, 100 mM tris(hydroxymethyl)aminomethane (pH 8.5), 200 mM sodium malonate/110 mM potassium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 1.70 Å R-free 0.228
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 2–456 Fragment:Heme-binding domain Mutation:F87A, A184K, T235A HEM PROTOPORPHYRIN IX CONTAINING FE × 1 SYN ethenylbenzene × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;277 K;300 mM magnesium formate, 100 mM tris(hydroxymethyl)aminomethane (pH 8.5), 200 mM sodium malonate/110 mM potassium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 1.70 Å R-free 0.228

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 1–455; UniProt 2–456 Author chain B; PDBConstruct 1–455; UniProt 2–456

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 4hgf

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4hgf
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id4hgf
Deposition date deposition_date2012-10-08
Structure title titleCrystal structure of P450 BM3 5F5K heme domain variant complexed with styrene
Keywords keywordsoxidoreductase, P450 BM3, hemoprotein, styrene epoxidation, inverted enantioselectivity, Heme binding; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier34.17
Radius of gyration Rg (electron density) rg_electron33.75
Forward intensity I(0) i0155843000.00
Molecular weight molecular_weight102490.0 kDa
Excluded volume excluded_volume129180 ų
Envelope volume envelope_volume162130 ų
Hydration-shell volume shell_volume40997 ų
Envelope diameter envelope_diameter130.5
Shell Rg shell_rg39.36
Envelope Rg envelope_rg33.65
Shape Rg shape_rg33.74
Total Rg total_rg34.19
Total atoms total_atoms7220
Residues n_residues883
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 dmax116.6
Rg (real space) rg_real34.33
Rg uncertainty (real space) rg_real_error0.87
I(0) (real space) i0_real1.5580e+08
I(0) uncertainty (real space) i0_real_error2.5420e+06
Rg (reciprocal space) rg_reciprocal34.23
I(0) (reciprocal space) i0_reciprocal155800000.0000
Solution quality estimate total_estimate0.8608
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary35.5
Skewness Skewness skewness0.496
Kurtosis Kurtosis kurtosis-0.301
Angular range angular_range— – 0.2300 −1
Current regularization parameter α current_alpha0.0003
Highest regularization parameter α highest_alpha34390000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.772; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.957; Smooth: 0.913

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_idd4hgfa_
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_idd4hgfb_
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_id4hgfA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450
Domain ID domain_id4hgfB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450

8. Citations (2)

9. Files and Curves (10)