5e7y

Crystal structure of P450 BM3 heme domain M7 variant

Method: X-RAY DIFFRACTION Dmax: 115.0 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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 2–472 Chain B; UniProt 2–472 Mutation:F87A V281G M354S HEM PROTOPORPHYRIN IX CONTAINING FE × 2 GOL GLYCEROL × 8 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;277 K;100-160 mM MgCl2 100mM MES 6.5 10-18% PEG3350 Resolution 2.00 Å R-free 0.220

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 311 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 1–471; UniProt 2–472 Author chain B; PDBConstruct 1–471; UniProt 2–472

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 5e7y

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5e7y
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5e7y
Deposition date deposition_date2015-10-13
Structure title titleCrystal structure of P450 BM3 heme domain M7 variant
Keywords keywordsBM3, P450, mediated electron transport, Co(III)Sep, oxidoreductase; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier34.35
Radius of gyration Rg (electron density) rg_electron33.90
Forward intensity I(0) i0165544000.00
Molecular weight molecular_weight104970.0 kDa
Excluded volume excluded_volume131950 ų
Envelope volume envelope_volume163290 ų
Hydration-shell volume shell_volume40890 ų
Envelope diameter envelope_diameter121.8
Shell Rg shell_rg39.70
Envelope Rg envelope_rg33.88
Shape Rg shape_rg33.91
Total Rg total_rg34.30
Total atoms total_atoms7395
Residues n_residues903
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 dmax115.0
Rg (real space) rg_real34.50
Rg uncertainty (real space) rg_real_error0.77
I(0) (real space) i0_real1.6550e+08
I(0) uncertainty (real space) i0_real_error2.8550e+06
Rg (reciprocal space) rg_reciprocal34.41
I(0) (reciprocal space) i0_reciprocal165500000.0000
Solution quality estimate total_estimate0.8621
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary35.0
Skewness Skewness skewness0.481
Kurtosis Kurtosis kurtosis-0.345
Angular range angular_range— – 0.2300 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha38180000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.799; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.964; Smooth: 0.842

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd5e7ya_
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_idd5e7yb_
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_id5e7yA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450
Domain ID domain_id5e7yB00
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)