5jqu

Crystal structure of Cytochrome P450 BM3 heme domain G265F/T269V/L272W/L322I/F405M/A406S (WIVS-FM) variant with iron(III) deuteroporphyrin IX bound

Method: X-RAY DIFFRACTION Dmax: 163.2 Å Quality: GOOD

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

Bifunctional cytochrome P450/NADPH--P450 reductase

Bacillus megaterium (strain ATCC 14581 / DSM 32 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / VKM B-512)

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 × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain A; UniProt 2–464 Chain B; UniProt 2–464 Chain C; UniProt 2–464 Chain D; UniProt 2–464 Chain E; UniProt 2–464 Chain F; UniProt 2–464 Chain G; UniProt 2–464 Chain H; UniProt 2–464 Fragment:heme domain, residues 2-456 Mutation:G265F,T269V,L272W,L322I,F405M,A406S FDE FE(III) DEUTEROPORPHYRIN IX × 8 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 7.5;298 K;0.25 M MgCl2, 17% PEG3350 Resolution 2.16 Å R-free 0.334

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_BACMB
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–463; UniProt 2–464 Author chain B; PDBConstruct 1–463; UniProt 2–464 Author chain C; PDBConstruct 1–463; UniProt 2–464 Author chain D; PDBConstruct 1–463; UniProt 2–464 Author chain E; PDBConstruct 1–463; UniProt 2–464 Author chain F; PDBConstruct 1–463; UniProt 2–464 Author chain G; PDBConstruct 1–463; UniProt 2–464 Author chain H; PDBConstruct 1–463; UniProt 2–464

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 5jqu

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id5jqu
Deposition date deposition_date2016-05-05
Structure title titleCrystal structure of Cytochrome P450 BM3 heme domain G265F/T269V/L272W/L322I/F405M/A406S (WIVS-FM) variant with iron(III) deuteroporphyrin IX bound
Keywords keywordsP450 BM3, iron(III) deuteroporphyrin IX, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier51.05
Radius of gyration Rg (electron density) rg_electron50.57
Forward intensity I(0) i02268710000.00
Molecular weight molecular_weight406850.0 kDa
Excluded volume excluded_volume511770 ų
Envelope volume envelope_volume706570 ų
Hydration-shell volume shell_volume113460 ų
Envelope diameter envelope_diameter170.3
Shell Rg shell_rg57.40
Envelope Rg envelope_rg48.94
Shape Rg shape_rg50.56
Total Rg total_rg50.83
Total atoms total_atoms28704
Residues n_residues3619
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 dmax163.2
Rg (real space) rg_real50.84
Rg uncertainty (real space) rg_real_error1.74
I(0) (real space) i0_real2.2690e+09
I(0) uncertainty (real space) i0_real_error4.3290e+07
Rg (reciprocal space) rg_reciprocal51.22
I(0) (reciprocal space) i0_reciprocal2270000000.0000
Solution quality estimate total_estimate0.8815
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary68.4
Skewness Skewness skewness0.132
Kurtosis Kurtosis kurtosis-0.433
Angular range angular_range— – 0.1550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha293000000.0000
Real-space data points n_real_points32
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.877; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.850

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd5jqua_
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_idd5jqub_
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_idd5jquc_
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_idd5jqud_
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_idd5jque_
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_idd5jquf_
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_idd5jqug_
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_idd5jquh_
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 (8 domains)

Domain ID domain_id5jquA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450
Domain ID domain_id5jquB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450
Domain ID domain_id5jquC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450
Domain ID domain_id5jquD00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450
Domain ID domain_id5jquE00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450
Domain ID domain_id5jquF00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450
Domain ID domain_id5jquG00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450
Domain ID domain_id5jquH00
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)