7y9k

Crystal structure of P450 BM3-TMK from Bacillus megaterium

Method: X-RAY DIFFRACTION Dmax: 103.9 Å Quality: GOOD

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

Bifunctional cytochrome P450/NADPH--P450 reductase

Priestia 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 3–465 Mutation:E5K,L76Y,F88G,T439K HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;298 K;30% PEG 3350, 0.1 M MgCl2, 0.1 M HEPES pH 7.5 Resolution 2.23 Å R-free 0.208
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 3–465 Mutation:E5K,L76Y,F88G,T439K HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;298 K;30% PEG 3350, 0.1 M MgCl2, 0.1 M HEPES pH 7.5 Resolution 2.23 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_BACMB
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–465; UniProt 3–465 Author chain B; PDBConstruct 3–465; UniProt 3–465

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 7y9k

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7y9k
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7y9k
Deposition date deposition_date2022-06-25
Structure title titleCrystal structure of P450 BM3-TMK from Bacillus megaterium
Keywords keywordssynthesis, monooxygenase, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier32.14
Radius of gyration Rg (electron density) rg_electron31.16
Forward intensity I(0) i0167217000.00
Molecular weight molecular_weight104980.0 kDa
Excluded volume excluded_volume132090 ų
Envelope volume envelope_volume162650 ų
Hydration-shell volume shell_volume42788 ų
Envelope diameter envelope_diameter110.2
Shell Rg shell_rg38.84
Envelope Rg envelope_rg31.16
Shape Rg shape_rg31.17
Total Rg total_rg31.77
Total atoms total_atoms7398
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 dmax103.9
Rg (real space) rg_real32.10
Rg uncertainty (real space) rg_real_error0.71
I(0) (real space) i0_real1.6720e+08
I(0) uncertainty (real space) i0_real_error2.1900e+06
Rg (reciprocal space) rg_reciprocal32.12
I(0) (reciprocal space) i0_reciprocal167200000.0000
Solution quality estimate total_estimate0.8927
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary38.2
Skewness Skewness skewness0.306
Kurtosis Kurtosis kurtosis-0.438
Angular range angular_range— – 0.2450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha41330000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.894; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.920

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)