6nbl

Cytochrome P450cam-putidaredoxin complex bound to camphor and cyanide

Method: X-RAY DIFFRACTION Dmax: 117.3 Å Quality: GOOD

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–415 Mutation:C334A, K344C, C59S, C86S, C137S, C268S Putidaredoxin × 1 (P00259) HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CYN CYANIDE ION × 1 CAM CAMPHOR × 1 CA CALCIUM ION × 1 1N0 1,1'-hexane-1,6-diyldipyrrolidine-2,5-dione × 1 FES FE2/S2 (INORGANIC) CLUSTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;298 K;0.2 M calcium acetate hydrate, 14-22% PEG3350, pH 7.4, 50 mM KCN Resolution 2.15 Å R-free 0.254
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 1–415 Mutation:C334A, K344C, C59S, C86S, C137S, C268S Putidaredoxin × 1 (P00259) HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CYN CYANIDE ION × 1 CAM CAMPHOR × 1 CA CALCIUM ION × 1 1N0 1,1'-hexane-1,6-diyldipyrrolidine-2,5-dione × 1 FES FE2/S2 (INORGANIC) CLUSTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;298 K;0.2 M calcium acetate hydrate, 14-22% PEG3350, pH 7.4, 50 mM KCN Resolution 2.15 Å R-free 0.254

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 B; PDBConstruct 1–415; UniProt 1–415

Putidaredoxin

Pseudomonas putida

UniProt P00259

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 2–107 Mutation:D19C, C74S Camphor 5-monooxygenase × 1 (P00183) HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CYN CYANIDE ION × 1 CAM CAMPHOR × 1 CA CALCIUM ION × 1 1N0 1,1'-hexane-1,6-diyldipyrrolidine-2,5-dione × 1 FES FE2/S2 (INORGANIC) CLUSTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;298 K;0.2 M calcium acetate hydrate, 14-22% PEG3350, pH 7.4, 50 mM KCN Resolution 2.15 Å R-free 0.254
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 2–107 Mutation:D19C, C74S Camphor 5-monooxygenase × 1 (P00183) HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CYN CYANIDE ION × 1 CAM CAMPHOR × 1 CA CALCIUM ION × 1 1N0 1,1'-hexane-1,6-diyldipyrrolidine-2,5-dione × 1 FES FE2/S2 (INORGANIC) CLUSTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;298 K;0.2 M calcium acetate hydrate, 14-22% PEG3350, pH 7.4, 50 mM KCN Resolution 2.15 Å R-free 0.254

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.

19 other PDB entries and 40 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PUTX_PSEPU
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 7–112; UniProt 2–107 Author chain D; PDBConstruct 7–112; UniProt 2–107

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 6nbl

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6nbl
Deposition date deposition_date2018-12-07
Structure title titleCytochrome P450cam-putidaredoxin complex bound to camphor and cyanide
Keywords keywordsELECTRON TRANSPORT, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier35.83
Radius of gyration Rg (electron density) rg_electron35.32
Forward intensity I(0) i0212439000.00
Molecular weight molecular_weight116200.0 kDa
Excluded volume excluded_volume144720 ų
Envelope volume envelope_volume185250 ų
Hydration-shell volume shell_volume44419 ų
Envelope diameter envelope_diameter121.6
Shell Rg shell_rg41.12
Envelope Rg envelope_rg35.00
Shape Rg shape_rg35.31
Total Rg total_rg35.76
Total atoms total_atoms8150
Residues n_residues1021
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 dmax117.3
Rg (real space) rg_real35.93
Rg uncertainty (real space) rg_real_error0.81
I(0) (real space) i0_real2.1240e+08
I(0) uncertainty (real space) i0_real_error3.2100e+06
Rg (reciprocal space) rg_reciprocal35.87
I(0) (reciprocal space) i0_reciprocal212400000.0000
Solution quality estimate total_estimate0.8723
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary37.3
Skewness Skewness skewness0.371
Kurtosis Kurtosis kurtosis-0.559
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha34180000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.852; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.957; Smooth: 0.822

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (9)

7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd6nbla_
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_idd6nblb_
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_idd6nblc_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.4 — 2Fe-2S ferredoxin-like
Family Family familyd.15.4.1 — 2Fe-2S ferredoxin-related
Domain ID domain_idd6nbld1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.4 — 2Fe-2S ferredoxin-like
Family Family familyd.15.4.1 — 2Fe-2S ferredoxin-related
Domain ID domain_idd6nbld2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id6nblA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450
Domain ID domain_id6nblB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450
Domain ID domain_id6nblC00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily30 — Beta-grasp domain
Domain ID domain_id6nblD00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily30 — Beta-grasp domain

8. Citations (1)

9. Files and Curves (10)