6iao

Structure of Cytochrome P450 BM3 M11 mutant in complex with DTT at resolution 2.16A

Method: X-RAY DIFFRACTION Dmax: 194.4 Å Quality: REASONABLE

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

Bifunctional cytochrome P450/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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–473 Chain B; UniProt 1–473 Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 2 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 3 CL CHLORIDE ION × 11 GOL GLYCEROL × 3 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;279 K;18% PEG4000, 0.25 M Magnesium chloride, 0.1 M TRIS pH 8.0, 10 mM DTT Resolution 2.16 Å R-free 0.202
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 1–473 Chain D; UniProt 1–473 Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 2 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 2 CL CHLORIDE ION × 9 GOL GLYCEROL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;279 K;18% PEG4000, 0.25 M Magnesium chloride, 0.1 M TRIS pH 8.0, 10 mM DTT Resolution 2.16 Å R-free 0.202

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 310 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CPXB_BACMB
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 35–507; UniProt 1–473 Author chain B; PDBConstruct 35–507; UniProt 1–473 Author chain C; PDBConstruct 35–507; UniProt 1–473 Author chain D; PDBConstruct 35–507; UniProt 1–473

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 6iao

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6iao
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6iao
Deposition date deposition_date2018-11-27
Structure title titleStructure of Cytochrome P450 BM3 M11 mutant in complex with DTT at resolution 2.16A
Keywords keywordsCytochrome P450 BM3, mutant M11, DTT, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier62.69
Radius of gyration Rg (electron density) rg_electron63.67
Forward intensity I(0) i0605798000.00
Molecular weight molecular_weight209720.0 kDa
Excluded volume excluded_volume263620 ų
Envelope volume envelope_volume411050 ų
Hydration-shell volume shell_volume56943 ų
Envelope diameter envelope_diameter204.2
Shell Rg shell_rg58.38
Envelope Rg envelope_rg61.33
Shape Rg shape_rg63.67
Total Rg total_rg63.52
Total atoms total_atoms14720
Residues n_residues1807
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 dmax194.4
Rg (real space) rg_real63.58
Rg uncertainty (real space) rg_real_error1.88
I(0) (real space) i0_real6.0580e+08
I(0) uncertainty (real space) i0_real_error1.2230e+07
Rg (reciprocal space) rg_reciprocal61.85
I(0) (reciprocal space) i0_reciprocal604000000.0000
Solution quality estimate total_estimate0.7319
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary31.1
Skewness Skewness skewness0.414
Kurtosis Kurtosis kurtosis-0.715
Angular range angular_range— – 0.1250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12870000.0000
Real-space data points n_real_points26
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.631; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.618; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd6iaoa_
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_idd6iaob_
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_idd6iaoc1
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_idd6iaoc2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd6iaod_
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_id6iaoA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450
Domain ID domain_id6iaoB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450
Domain ID domain_id6iaoC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450
Domain ID domain_id6iaoD00
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)