2qbm

Crystal structure of the P450cam G248T mutant in the cyanide bound state

Method: X-RAY DIFFRACTION Dmax: 69.4 Å Quality: EXCELLENT

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 1–415 Mutation:G248T CYN CYANIDE ION × 1 K POTASSIUM ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CAM CAMPHOR × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.4;277 K;1 UL OF 15 MG/ML P450 IN 50 MM Potassium phosphate, 250 MM KCL WERE MIXED WITH AN EQUAL VOLUME OF THE RESERVOIR SOLUTION (100 mM Tris, 250 mM KCl, 27-30% PEG 8000, 100 MM DTE), pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 1.80 Å R-free 0.220

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 172 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

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 2qbm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2qbm
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2qbm
Deposition date deposition_date2007-06-18
Structure title titleCrystal structure of the P450cam G248T mutant in the cyanide bound state
Keywords keywordsCYP101, mutant, conserved active site residue, cyanide complex, Gly248, heme geometry, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier22.38
Radius of gyration Rg (electron density) rg_electron21.16
Forward intensity I(0) i035901600.00
Molecular weight molecular_weight46437.0 kDa
Excluded volume excluded_volume58157 ų
Envelope volume envelope_volume65525 ų
Hydration-shell volume shell_volume25279 ų
Envelope diameter envelope_diameter70.5
Shell Rg shell_rg28.50
Envelope Rg envelope_rg21.48
Shape Rg shape_rg21.16
Total Rg total_rg22.03
Total atoms total_atoms3267
Residues n_residues405
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 dmax69.4
Rg (real space) rg_real22.27
Rg uncertainty (real space) rg_real_error0.31
I(0) (real space) i0_real3.5900e+07
I(0) uncertainty (real space) i0_real_error4.1990e+05
Rg (reciprocal space) rg_reciprocal22.30
I(0) (reciprocal space) i0_reciprocal35900000.0000
Solution quality estimate total_estimate0.9031
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.3
Skewness Skewness skewness0.184
Kurtosis Kurtosis kurtosis-0.472
Angular range angular_range— – 0.3550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7967000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.921; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.983

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2qbma_
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 (1 domains)

Domain ID domain_id2qbmA00
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)