1dz8

oxygen complex of p450cam from pseudomonas putida

Method: X-RAY DIFFRACTION Dmax: 109.3 Å Quality: GOOD

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

CYTOCHROME P450-CAM

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 1–414 Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 1 OXY OXYGEN MOLECULE × 1 CAM CAMPHOR × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.4;275 K;CRYSTALS WERE GROWN USING THE SITTING DROP GEOMETRY AT 2 DEG. C. 5 UL OF 30 MG/ML P450 IN 50 MM TRIS HCL, 250 MM KCL, 0.5 MM CAMPHOR WERE MIXED WITH AN EQUAL VOLUME OF THE RESERVOIR SOLUTION (27-30% PEG 4000, 100 MM DTE, SAME BUFFER AS PROTEIN)., pH 7.40 Resolution 1.90 Å R-free 0.248
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1–414 Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CAM CAMPHOR × 1 K POTASSIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.4;275 K;CRYSTALS WERE GROWN USING THE SITTING DROP GEOMETRY AT 2 DEG. C. 5 UL OF 30 MG/ML P450 IN 50 MM TRIS HCL, 250 MM KCL, 0.5 MM CAMPHOR WERE MIXED WITH AN EQUAL VOLUME OF THE RESERVOIR SOLUTION (27-30% PEG 4000, 100 MM DTE, SAME BUFFER AS PROTEIN)., pH 7.40 Resolution 1.90 Å R-free 0.248

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 1–414 Author chain B; PDBConstruct 1–414; UniProt 1–414

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 1dz8

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1dz8
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1dz8
Deposition date deposition_date2000-02-18
Structure title titleoxygen complex of p450cam from pseudomonas putida
Keywords keywordsOXIDOREDUCTASE, MONO-OXYGENASE, HEME; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier33.68
Radius of gyration Rg (electron density) rg_electron33.25
Forward intensity I(0) i0132450000.00
Molecular weight molecular_weight92847.0 kDa
Excluded volume excluded_volume116330 ų
Envelope volume envelope_volume140390 ų
Hydration-shell volume shell_volume36501 ų
Envelope diameter envelope_diameter118.2
Shell Rg shell_rg38.43
Envelope Rg envelope_rg33.15
Shape Rg shape_rg33.28
Total Rg total_rg33.56
Total atoms total_atoms6529
Residues n_residues809
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 dmax109.3
Rg (real space) rg_real33.84
Rg uncertainty (real space) rg_real_error0.97
I(0) (real space) i0_real1.3240e+08
I(0) uncertainty (real space) i0_real_error2.1730e+06
Rg (reciprocal space) rg_reciprocal33.74
I(0) (reciprocal space) i0_reciprocal132400000.0000
Solution quality estimate total_estimate0.8488
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.2
Skewness Skewness skewness0.446
Kurtosis Kurtosis kurtosis-0.502
Angular range angular_range— – 0.2350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha39490000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.844; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.854; Smooth: 0.646

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1dz8a_
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_idd1dz8b_
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_id1dz8A00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450
Domain ID domain_id1dz8B00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450

8. Citations (3)

9. Files and Curves (10)