5gxg

High-resolution crystal structure of the electron transfer complex of cytochrome p450cam with putidaredoxin

Method: X-RAY DIFFRACTION Dmax: 72.2 Å Quality: EXCELLENT

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 2–415 Mutation:K126C,R130C, C334A Putidaredoxin × 1 (P00259) HEM PROTOPORPHYRIN IX CONTAINING FE × 1 SO4 SULFATE ION × 5 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 FES FE2/S2 (INORGANIC) CLUSTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;289 K;0.1M HEPES, 0.1M Sodium Chloride, 1.6M Ammonium sulfate Resolution 1.70 Å R-free 0.192
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 2–415 Mutation:K126C,R130C, C334A Putidaredoxin × 2 (P00259) HEM PROTOPORPHYRIN IX CONTAINING FE × 2 SO4 SULFATE ION × 10 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;289 K;0.1M HEPES, 0.1M Sodium Chloride, 1.6M Ammonium sulfate Resolution 1.70 Å R-free 0.192

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 3–416; UniProt 2–415

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 B; UniProt 2–107 Not recorded Camphor 5-monooxygenase × 1 (P00183) HEM PROTOPORPHYRIN IX CONTAINING FE × 1 SO4 SULFATE ION × 5 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 FES FE2/S2 (INORGANIC) CLUSTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;289 K;0.1M HEPES, 0.1M Sodium Chloride, 1.6M Ammonium sulfate Resolution 1.70 Å R-free 0.192
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 2–107 Not recorded Camphor 5-monooxygenase × 2 (P00183) HEM PROTOPORPHYRIN IX CONTAINING FE × 2 SO4 SULFATE ION × 10 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;289 K;0.1M HEPES, 0.1M Sodium Chloride, 1.6M Ammonium sulfate Resolution 1.70 Å R-free 0.192

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 B; PDBConstruct 3–108; 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 5gxg

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5gxg
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5gxg
Deposition date deposition_date2016-09-17
Structure title titleHigh-resolution crystal structure of the electron transfer complex of cytochrome p450cam with putidaredoxin
Keywords keywordsinter-protein electron transfer, 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_guinier24.26
Radius of gyration Rg (electron density) rg_electron23.06
Forward intensity I(0) i058568800.00
Molecular weight molecular_weight57974.0 kDa
Excluded volume excluded_volume71777 ų
Envelope volume envelope_volume83732 ų
Hydration-shell volume shell_volume29483 ų
Envelope diameter envelope_diameter71.8
Shell Rg shell_rg30.80
Envelope Rg envelope_rg23.23
Shape Rg shape_rg23.08
Total Rg total_rg23.82
Total atoms total_atoms4050
Residues n_residues507
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 dmax72.2
Rg (real space) rg_real24.07
Rg uncertainty (real space) rg_real_error0.35
I(0) (real space) i0_real5.8570e+07
I(0) uncertainty (real space) i0_real_error6.8740e+05
Rg (reciprocal space) rg_reciprocal24.12
I(0) (reciprocal space) i0_reciprocal58570000.0000
Solution quality estimate total_estimate0.9115
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.9
Skewness Skewness skewness0.088
Kurtosis Kurtosis kurtosis-0.567
Angular range angular_range— – 0.3250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11020000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.960; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.979

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd5gxga_
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_idd5gxgb_
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 (2 domains)

Domain ID domain_id5gxgA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450
Domain ID domain_id5gxgB00
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)