8yb2

XFEL crystal structure of the oxygen-bound form of F393H P450BM3 with N-enanthyl-L-prolyl-L-phenylalanine in complex with styrene

Method: X-RAY DIFFRACTION Dmax: 120.2 Å Quality: GOOD

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

Bifunctional cytochrome P450/NADPH--P450 reductase

Priestia megaterium NBRC 15308 = ATCC 14581

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 Mutation:F393H HEM PROTOPORPHYRIN IX CONTAINING FE × 1 D0L (2S)-2-[[(2S)-1-heptylpyrrolidin-2-yl]carbonylamino]-3-phenyl-propanoic acid × 1 SYN ethenylbenzene × 1 OXY OXYGEN MOLECULE × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION X-ray crystallization conditions:BATCH MODE;pH 7.4;277 K;50 mM Tris-HCl buffer, 120 mM MgCl2, 16-18% PEG 8000, 200 uM N-Enanthyl-L-Prolyl-L-Phenylalanine, 1%(v/v) styrene Resolution 1.50 Å R-free 0.208
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 2–456 Mutation:F393H HEM PROTOPORPHYRIN IX CONTAINING FE × 1 D0L (2S)-2-[[(2S)-1-heptylpyrrolidin-2-yl]carbonylamino]-3-phenyl-propanoic acid × 1 SYN ethenylbenzene × 1 OXY OXYGEN MOLECULE × 1 GOL GLYCEROL × 5 X-RAY DIFFRACTION X-ray crystallization conditions:BATCH MODE;pH 7.4;277 K;50 mM Tris-HCl buffer, 120 mM MgCl2, 16-18% PEG 8000, 200 uM N-Enanthyl-L-Prolyl-L-Phenylalanine, 1%(v/v) styrene Resolution 1.50 Å R-free 0.208

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_PRIM2
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 8yb2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8yb2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8yb2
Deposition date deposition_date2024-02-11
Structure title titleXFEL crystal structure of the oxygen-bound form of F393H P450BM3 with N-enanthyl-L-prolyl-L-phenylalanine in complex with styrene
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_guinier34.21
Radius of gyration Rg (electron density) rg_electron33.76
Forward intensity I(0) i0169578000.00
Molecular weight molecular_weight107120.0 kDa
Excluded volume excluded_volume134950 ų
Envelope volume envelope_volume163160 ų
Hydration-shell volume shell_volume40843 ų
Envelope diameter envelope_diameter128.8
Shell Rg shell_rg39.81
Envelope Rg envelope_rg33.80
Shape Rg shape_rg33.76
Total Rg total_rg34.20
Total atoms total_atoms7610
Residues n_residues910
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 dmax120.2
Rg (real space) rg_real34.36
Rg uncertainty (real space) rg_real_error0.93
I(0) (real space) i0_real1.6960e+08
I(0) uncertainty (real space) i0_real_error2.8730e+06
Rg (reciprocal space) rg_reciprocal34.27
I(0) (reciprocal space) i0_reciprocal169600000.0000
Solution quality estimate total_estimate0.8481
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary34.0
Skewness Skewness skewness0.471
Kurtosis Kurtosis kurtosis-0.369
Angular range angular_range— – 0.2300 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha43670000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.709; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.925; Smooth: 0.969

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

8. Citations (1)

9. Files and Curves (10)