7ydc

Crystal structure of the P450 BM3 heme domain mutant F87L/T268V/V78C in complex with N-imidazolyl-pentanoyl-L-phenylalanine and hydroxylamine

Method: X-RAY DIFFRACTION Dmax: 100.1 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 1–456 Mutation:V78C,F87L,T268V HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HOA HYDROXYAMINE × 1 IRV (2~{S})-2-(5-imidazol-1-ylpentanoylamino)-3-phenyl-propanoic acid × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;291 K;0.2 M Ammonium acetate, 0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES pH7.5, 25% PEG3350 Resolution 1.61 Å R-free 0.191
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1–456 Mutation:V78C,F87L,T268V HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HOA HYDROXYAMINE × 1 IRV (2~{S})-2-(5-imidazol-1-ylpentanoylamino)-3-phenyl-propanoic acid × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;291 K;0.2 M Ammonium acetate, 0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES pH7.5, 25% PEG3350 Resolution 1.61 Å R-free 0.191

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_BACMB
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–458; UniProt 1–456 Author chain B; PDBConstruct 3–458; 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 7ydc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7ydc
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7ydc
Deposition date deposition_date2022-07-04
Structure title titleCrystal structure of the P450 BM3 heme domain mutant F87L/T268V/V78C in complex with N-imidazolyl-pentanoyl-L-phenylalanine and hydroxylamine
Keywords keywordsP450 BM3 heme domain, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier31.74
Radius of gyration Rg (electron density) rg_electron30.72
Forward intensity I(0) i0168919000.00
Molecular weight molecular_weight105680.0 kDa
Excluded volume excluded_volume132990 ų
Envelope volume envelope_volume160680 ų
Hydration-shell volume shell_volume42720 ų
Envelope diameter envelope_diameter108.7
Shell Rg shell_rg38.67
Envelope Rg envelope_rg30.74
Shape Rg shape_rg30.73
Total Rg total_rg31.34
Total atoms total_atoms7551
Residues n_residues907
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 dmax100.1
Rg (real space) rg_real31.68
Rg uncertainty (real space) rg_real_error0.63
I(0) (real space) i0_real1.6890e+08
I(0) uncertainty (real space) i0_real_error2.4900e+06
Rg (reciprocal space) rg_reciprocal31.71
I(0) (reciprocal space) i0_reciprocal168900000.0000
Solution quality estimate total_estimate0.8982
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary38.0
Skewness Skewness skewness0.294
Kurtosis Kurtosis kurtosis-0.437
Angular range angular_range— – 0.2500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha46330000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.924; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.902

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)