3wrk

Crystal structure of P450cam

Method: X-RAY DIFFRACTION Dmax: 96.3 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 1–415 Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CAM CAMPHOR × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;279 K;50mM Tris-HCl, 200mM KCl, 20-30% PEG 4000, 0.00025mM Camphor, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 279K Resolution 2.61 Å R-free 0.235
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 1–415 Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CAM CAMPHOR × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;279 K;50mM Tris-HCl, 200mM KCl, 20-30% PEG 4000, 0.00025mM Camphor, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 279K Resolution 2.61 Å R-free 0.235

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 1–415; UniProt 1–415 Author chain D; PDBConstruct 1–415; UniProt 1–415

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 3wrk

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3wrk
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id3wrk
Deposition date deposition_date2014-02-25
Structure title titleCrystal structure of P450cam
Keywords keywordsOXIDOREDUCTASE, Metal-binding; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier30.57
Radius of gyration Rg (electron density) rg_electron29.49
Forward intensity I(0) i0128373000.00
Molecular weight molecular_weight89799.0 kDa
Excluded volume excluded_volume112440 ų
Envelope volume envelope_volume139450 ų
Hydration-shell volume shell_volume38801 ų
Envelope diameter envelope_diameter100.5
Shell Rg shell_rg37.42
Envelope Rg envelope_rg29.16
Shape Rg shape_rg29.51
Total Rg total_rg30.17
Total atoms total_atoms6325
Residues n_residues783
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 dmax96.3
Rg (real space) rg_real30.45
Rg uncertainty (real space) rg_real_error0.60
I(0) (real space) i0_real1.2840e+08
I(0) uncertainty (real space) i0_real_error1.6820e+06
Rg (reciprocal space) rg_reciprocal30.51
I(0) (reciprocal space) i0_reciprocal128400000.0000
Solution quality estimate total_estimate0.9076
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary38.9
Skewness Skewness skewness0.186
Kurtosis Kurtosis kurtosis-0.561
Angular range angular_range— – 0.2600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha30660000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.940; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.973

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3wrka1
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_idd3wrka2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3wrkd1
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_idd3wrkd2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id3wrkA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450
Domain ID domain_id3wrkD00
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)