1smj

Structure of the A264E mutant of cytochrome P450 BM3 complexed with palmitoleate

Method: X-RAY DIFFRACTION Dmax: 186.7 Å Quality: REASONABLE

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 1–471 Fragment:cytochrome P450 102 Mutation:A264E HEM PROTOPORPHYRIN IX CONTAINING FE × 1 PAM PALMITOLEIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.3;277 K;PEG 2000, MME, 100mM magnesium acetate, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.75 Å R-free 0.338
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1–471 Fragment:cytochrome P450 102 Mutation:A264E HEM PROTOPORPHYRIN IX CONTAINING FE × 1 PAM PALMITOLEIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.3;277 K;PEG 2000, MME, 100mM magnesium acetate, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.75 Å R-free 0.338
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 1–471 Fragment:cytochrome P450 102 Mutation:A264E HEM PROTOPORPHYRIN IX CONTAINING FE × 1 PAM PALMITOLEIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.3;277 K;PEG 2000, MME, 100mM magnesium acetate, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.75 Å R-free 0.338
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 1–471 Fragment:cytochrome P450 102 Mutation:A264E HEM PROTOPORPHYRIN IX CONTAINING FE × 1 PAM PALMITOLEIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.3;277 K;PEG 2000, MME, 100mM magnesium acetate, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.75 Å R-free 0.338

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 308 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 1–471 Author chain B; PDBConstruct 1–471; UniProt 1–471 Author chain C; PDBConstruct 1–471; UniProt 1–471 Author chain D; PDBConstruct 1–471; UniProt 1–471

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 1smj

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1smj
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1smj
Deposition date deposition_date2004-03-09
Structure title titleStructure of the A264E mutant of cytochrome P450 BM3 complexed with palmitoleate
Keywords keywordsmonooxygenase; fatty acid oxygenase; cytochrome P450; substrate binding; palmitoleate, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier66.16
Radius of gyration Rg (electron density) rg_electron66.18
Forward intensity I(0) i0596931000.00
Molecular weight molecular_weight211600.0 kDa
Excluded volume excluded_volume266670 ų
Envelope volume envelope_volume437370 ų
Hydration-shell volume shell_volume55812 ų
Envelope diameter envelope_diameter199.7
Shell Rg shell_rg70.00
Envelope Rg envelope_rg61.27
Shape Rg shape_rg66.18
Total Rg total_rg66.25
Total atoms total_atoms14913
Residues n_residues1819
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 dmax186.7
Rg (real space) rg_real66.36
Rg uncertainty (real space) rg_real_error1.88
I(0) (real space) i0_real5.9690e+08
I(0) uncertainty (real space) i0_real_error1.2340e+07
Rg (reciprocal space) rg_reciprocal65.86
I(0) (reciprocal space) i0_reciprocal596300000.0000
Solution quality estimate total_estimate0.6799
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.1
Skewness Skewness skewness0.015
Kurtosis Kurtosis kurtosis-1.050
Angular range angular_range— – 0.1200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12140000.0000
Real-space data points n_real_points25
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.418; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.583; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1smja_
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_idd1smjb_
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_idd1smjc_
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_idd1smjd_
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 (4 domains)

Domain ID domain_id1smjA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450
Domain ID domain_id1smjB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450
Domain ID domain_id1smjC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450
Domain ID domain_id1smjD00
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)