2m56

The structure of the complex of cytochrome P450cam and its electron donor putidaredoxin determined by paramagnetic NMR spectroscopy

Method: SOLUTION NMR Dmax: 64.0 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 12–415 Fragment:UNP RESIDUES 12-415 Putidaredoxin × 1 (P00259) HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CAM CAMPHOR × 1 FES FE2/S2 (INORGANIC) CLUSTER × 1 SOLUTION NMR NMR measurement conditions:pH 7.4;290 K;Ionic strength (raw mmCIF value) 100;Pressure ambient NMR sample composition:100 uM [U-95% 15N] entity_1-1, 93% H2O/7% D2O | 93% H2O/7% D2O Resolution not provided

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 172 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 1–404; UniProt 12–415

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 Mutation:C74S Camphor 5-monooxygenase × 1 (P00183) HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CAM CAMPHOR × 1 FES FE2/S2 (INORGANIC) CLUSTER × 1 SOLUTION NMR NMR measurement conditions:pH 7.4;290 K;Ionic strength (raw mmCIF value) 100;Pressure ambient NMR sample composition:100 uM [U-95% 15N] entity_1-1, 93% H2O/7% D2O | 93% H2O/7% D2O Resolution not provided

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 41 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 1–106; 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 2m56

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2m56
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2m56
Deposition date deposition_date2013-02-14
Structure title titleThe structure of the complex of cytochrome P450cam and its electron donor putidaredoxin determined by paramagnetic NMR spectroscopy
Keywords keywordscamphor, heme, iron-sulphor, lanthanide, paramagnetic, electron transfer, ferredoxin, OXIDOREDUCTASE-METAL BINDING PROTEIN complex; OXIDOREDUCTASE/METAL BINDING PROTEIN
Experimental Method methodSOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier23.37
Radius of gyration Rg (electron density) rg_electron22.98
Forward intensity I(0) i04725630000.00
Molecular weight molecular_weight578010.0 kDa
Excluded volume excluded_volume719950 ų
Envelope volume envelope_volume89285 ų
Hydration-shell volume shell_volume30815 ų
Envelope diameter envelope_diameter73.3
Shell Rg shell_rg31.52
Envelope Rg envelope_rg23.64
Shape Rg shape_rg23.00
Total Rg total_rg23.00
Total atoms total_atoms79770
Residues n_residues5100
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 dmax64.0
Rg (real space) rg_real23.20
Rg uncertainty (real space) rg_real_error0.24
I(0) (real space) i0_real4.7260e+09
I(0) uncertainty (real space) i0_real_error5.5840e+07
Rg (reciprocal space) rg_reciprocal23.24
I(0) (reciprocal space) i0_reciprocal4726000000.0000
Solution quality estimate total_estimate0.8864
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.6
Skewness Skewness skewness0.071
Kurtosis Kurtosis kurtosis-0.598
Angular range angular_range— – 0.3400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7270000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.997; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.536

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2m56a_
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_idd2m56b_
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_id2m56A00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450
Domain ID domain_id2m56B00
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)