4jx1

Crystal structure of reduced Cytochrome P450cam-putidaredoxin complex bound to camphor and 5-exo-hydroxycamphor

Method: X-RAY DIFFRACTION Dmax: 157.0 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:K344C, C334A, C59S, C86S, C137S, C286S Putidaredoxin × 1 (P00259) HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CAM CAMPHOR × 1 CAH 5-EXO-HYDROXYCAMPHOR × 1 CA CALCIUM ION × 1 FES FE2/S2 (INORGANIC) CLUSTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;298 K;0.2 M calcium acetate hydrate, 14-22% PEG3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.09 Å R-free 0.212
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 1–415 Mutation:K344C, C334A, C59S, C86S, C137S, C286S Putidaredoxin × 1 (P00259) HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CAM CAMPHOR × 1 CA CALCIUM ION × 1 FES FE2/S2 (INORGANIC) CLUSTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;298 K;0.2 M calcium acetate hydrate, 14-22% PEG3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.09 Å R-free 0.212
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain E; UniProt 1–415 Mutation:K344C, C334A, C59S, C86S, C137S, C286S Putidaredoxin × 1 (P00259) HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CAM CAMPHOR × 1 CAH 5-EXO-HYDROXYCAMPHOR × 1 CA CALCIUM ION × 1 FES FE2/S2 (INORGANIC) CLUSTER × 1 1N0 1,1'-hexane-1,6-diyldipyrrolidine-2,5-dione × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;298 K;0.2 M calcium acetate hydrate, 14-22% PEG3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.09 Å R-free 0.212
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain F; UniProt 1–415 Mutation:K344C, C334A, C59S, C86S, C137S, C286S Putidaredoxin × 1 (P00259) HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CAM CAMPHOR × 1 CAH 5-EXO-HYDROXYCAMPHOR × 1 CA CALCIUM ION × 1 FES FE2/S2 (INORGANIC) CLUSTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;298 K;0.2 M calcium acetate hydrate, 14-22% PEG3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.09 Å R-free 0.212

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 169 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 Author chain E; PDBConstruct 1–415; UniProt 1–415 Author chain F; 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 1–107 Mutation:C85S, C73S, D19C Camphor 5-monooxygenase × 1 (P00183) HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CAM CAMPHOR × 1 CAH 5-EXO-HYDROXYCAMPHOR × 1 CA CALCIUM ION × 1 FES FE2/S2 (INORGANIC) CLUSTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;298 K;0.2 M calcium acetate hydrate, 14-22% PEG3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.09 Å R-free 0.212
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 1–107 Mutation:C85S, C73S, D19C Camphor 5-monooxygenase × 1 (P00183) HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CAM CAMPHOR × 1 CA CALCIUM ION × 1 FES FE2/S2 (INORGANIC) CLUSTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;298 K;0.2 M calcium acetate hydrate, 14-22% PEG3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.09 Å R-free 0.212
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain G; UniProt 1–107 Mutation:C85S, C73S, D19C Camphor 5-monooxygenase × 1 (P00183) HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CAM CAMPHOR × 1 CAH 5-EXO-HYDROXYCAMPHOR × 1 CA CALCIUM ION × 1 FES FE2/S2 (INORGANIC) CLUSTER × 1 1N0 1,1'-hexane-1,6-diyldipyrrolidine-2,5-dione × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;298 K;0.2 M calcium acetate hydrate, 14-22% PEG3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.09 Å R-free 0.212
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain H; UniProt 1–107 Mutation:C85S, C73S, D19C Camphor 5-monooxygenase × 1 (P00183) HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CAM CAMPHOR × 1 CAH 5-EXO-HYDROXYCAMPHOR × 1 CA CALCIUM ION × 1 FES FE2/S2 (INORGANIC) CLUSTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;298 K;0.2 M calcium acetate hydrate, 14-22% PEG3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.09 Å R-free 0.212

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 38 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 7–113; UniProt 1–107 Author chain D; PDBConstruct 7–113; UniProt 1–107 Author chain G; PDBConstruct 7–113; UniProt 1–107 Author chain H; PDBConstruct 7–113; UniProt 1–107

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 4jx1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4jx1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4jx1
Deposition date deposition_date2013-03-27
Structure title titleCrystal structure of reduced Cytochrome P450cam-putidaredoxin complex bound to camphor and 5-exo-hydroxycamphor
Keywords keywordsreduced P450cam-Pdx complex, redox partners, OXIDOREDUCTASE-ELECTRON TRANSPORT complex; OXIDOREDUCTASE/ELECTRON TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier45.45
Radius of gyration Rg (electron density) rg_electron45.15
Forward intensity I(0) i0803288000.00
Molecular weight molecular_weight231900.0 kDa
Excluded volume excluded_volume289040 ų
Envelope volume envelope_volume384210 ų
Hydration-shell volume shell_volume71494 ų
Envelope diameter envelope_diameter160.1
Shell Rg shell_rg49.22
Envelope Rg envelope_rg44.42
Shape Rg shape_rg45.14
Total Rg total_rg45.35
Total atoms total_atoms32165
Residues n_residues2044
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 dmax157.0
Rg (real space) rg_real45.51
Rg uncertainty (real space) rg_real_error1.63
I(0) (real space) i0_real8.0330e+08
I(0) uncertainty (real space) i0_real_error1.5420e+07
Rg (reciprocal space) rg_reciprocal45.45
I(0) (reciprocal space) i0_reciprocal803200000.0000
Solution quality estimate total_estimate0.8547
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary62.8
Skewness Skewness skewness0.377
Kurtosis Kurtosis kurtosis-0.203
Angular range angular_range— – 0.1750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha206500000.0000
Real-space data points n_real_points36
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.794; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.965; Smooth: 0.761

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (9)

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd4jx1a_
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_idd4jx1b_
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_idd4jx1c_
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_idd4jx1d_
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_idd4jx1e_
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_idd4jx1f_
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_idd4jx1g_
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_idd4jx1h_
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

CATH v4.4 (8 domains)

Domain ID domain_id4jx1A00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450
Domain ID domain_id4jx1B00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450
Domain ID domain_id4jx1C00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily30 — Beta-grasp domain
Domain ID domain_id4jx1D00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily30 — Beta-grasp domain
Domain ID domain_id4jx1E00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450
Domain ID domain_id4jx1F00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450
Domain ID domain_id4jx1G00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily30 — Beta-grasp domain
Domain ID domain_id4jx1H00
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)