6k9s

Structure of the Carbonylruthenium Mesoporphyrin IX-Reconstituted CYP102A1 Haem Domain with N-Abietoyl-L-Tryptophan

Method: X-RAY DIFFRACTION Dmax: 118.2 Å Quality: GOOD

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 1–456 Not recorded RUR [3,3'-(7,12-diethyl-3,8,13,17-tetramethylporphyrin-2,18-diyl-kappa~4~N~21~,N~22~,N~23~,N~24~)dipropanoato(2-)]ruthenium × 1 CMO CARBON MONOXIDE × 1 GOL GLYCEROL × 6 WAA (2S)-2-[[(1R,4aR,4bR,10aR)-1,4a-dimethyl-7-propan-2-yl-2,3,4,4b,5,6,10,10a-octahydrophenanthren-1-yl]carbonylamino]-3-( 1H-indol-3-yl)propanoic acid × 1 X-RAY DIFFRACTION X-ray crystallization conditions:BATCH MODE;293 K;PEG 8000, Magnesium Chloride, Tris-HCl. 0.5% DMSO, 125 uM N-Abietoyl-L-Tryptophan Resolution 1.55 Å R-free 0.205
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1–456 Not recorded RUR [3,3'-(7,12-diethyl-3,8,13,17-tetramethylporphyrin-2,18-diyl-kappa~4~N~21~,N~22~,N~23~,N~24~)dipropanoato(2-)]ruthenium × 1 CMO CARBON MONOXIDE × 1 GOL GLYCEROL × 7 WAA (2S)-2-[[(1R,4aR,4bR,10aR)-1,4a-dimethyl-7-propan-2-yl-2,3,4,4b,5,6,10,10a-octahydrophenanthren-1-yl]carbonylamino]-3-( 1H-indol-3-yl)propanoic acid × 1 X-RAY DIFFRACTION X-ray crystallization conditions:BATCH MODE;293 K;PEG 8000, Magnesium Chloride, Tris-HCl. 0.5% DMSO, 125 uM N-Abietoyl-L-Tryptophan Resolution 1.55 Å R-free 0.205

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 1–456; UniProt 1–456 Author chain B; PDBConstruct 1–456; UniProt 1–456

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 6k9s

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6k9s
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6k9s
Deposition date deposition_date2019-06-17
Structure title titleStructure of the Carbonylruthenium Mesoporphyrin IX-Reconstituted CYP102A1 Haem Domain with N-Abietoyl-L-Tryptophan
Keywords keywordsMonooxygenase, Oxidoreductase; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier34.35
Radius of gyration Rg (electron density) rg_electron33.91
Forward intensity I(0) i0167509000.00
Molecular weight molecular_weight106820.0 kDa
Excluded volume excluded_volume134720 ų
Envelope volume envelope_volume163810 ų
Hydration-shell volume shell_volume40810 ų
Envelope diameter envelope_diameter129.6
Shell Rg shell_rg39.84
Envelope Rg envelope_rg33.97
Shape Rg shape_rg33.91
Total Rg total_rg34.34
Total atoms total_atoms7518
Residues n_residues901
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 dmax118.2
Rg (real space) rg_real34.51
Rg uncertainty (real space) rg_real_error1.16
I(0) (real space) i0_real1.6750e+08
I(0) uncertainty (real space) i0_real_error2.8760e+06
Rg (reciprocal space) rg_reciprocal34.41
I(0) (reciprocal space) i0_reciprocal167500000.0000
Solution quality estimate total_estimate0.8533
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.4
Skewness Skewness skewness0.472
Kurtosis Kurtosis kurtosis-0.383
Angular range angular_range— – 0.2300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha40410000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.743; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.937; Smooth: 0.922

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_idd6k9sa_
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_idd6k9sb_
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_id6k9sA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450
Domain ID domain_id6k9sB00
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)