4ek1

Crystal Structure of Electron-Spin Labeled Cytochrome P450cam

Method: X-RAY DIFFRACTION Dmax: 87.8 Å Quality: EXCELLENT

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

Camphor 5-monooxygenase

Pseudomonas putida

UniProt P00183

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 2–415 Mutation:S48C,C58S,C85S,C136S,S190C,C285S,C334A HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CAM CAMPHOR × 1 K POTASSIUM ION × 1 MTN S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate × 2 X-RAY DIFFRACTION X-ray crystallization conditions:sitting-drop vapor diffusion;pH 7.4;279 K;12% PEG 8000, 0.1M Tris, pH 7.4, 0.2M KCl, 1mM camphor, sitting-drop vapor diffusion, temperature 279K Resolution 1.97 Å R-free 0.253
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 2–415 Mutation:S48C,C58S,C85S,C136S,S190C,C285S,C334A HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CAM CAMPHOR × 1 K POTASSIUM ION × 1 MTN S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate × 1 X-RAY DIFFRACTION X-ray crystallization conditions:sitting-drop vapor diffusion;pH 7.4;279 K;12% PEG 8000, 0.1M Tris, pH 7.4, 0.2M KCl, 1mM camphor, sitting-drop vapor diffusion, temperature 279K Resolution 1.97 Å R-free 0.253

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.

128 other PDB entries and 171 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CPXA_PSEPU
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–414; UniProt 2–415 Author chain B; PDBConstruct 1–414; UniProt 2–415

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 4ek1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4ek1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4ek1
Deposition date deposition_date2012-04-08
Structure title titleCrystal Structure of Electron-Spin Labeled Cytochrome P450cam
Keywords keywordselectron spin, MTSL, double electron electron resonance, camphor, Cytochrome P450 fold, Monooxidase, Putidaredoxin, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier29.26
Radius of gyration Rg (electron density) rg_electron28.09
Forward intensity I(0) i0136092000.00
Molecular weight molecular_weight92849.0 kDa
Excluded volume excluded_volume116440 ų
Envelope volume envelope_volume137710 ų
Hydration-shell volume shell_volume39539 ų
Envelope diameter envelope_diameter89.9
Shell Rg shell_rg36.62
Envelope Rg envelope_rg27.95
Shape Rg shape_rg28.09
Total Rg total_rg28.90
Total atoms total_atoms6536
Residues n_residues807
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 dmax87.8
Rg (real space) rg_real29.10
Rg uncertainty (real space) rg_real_error0.36
I(0) (real space) i0_real1.3610e+08
I(0) uncertainty (real space) i0_real_error1.5600e+06
Rg (reciprocal space) rg_reciprocal29.17
I(0) (reciprocal space) i0_reciprocal136100000.0000
Solution quality estimate total_estimate0.9105
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary37.4
Skewness Skewness skewness0.107
Kurtosis Kurtosis kurtosis-0.604
Angular range angular_range— – 0.2700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha34420000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.967; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.943

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4ek1a_
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_idd4ek1b_
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_id4ek1A00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450
Domain ID domain_id4ek1B00
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)