4egp

The X-ray crystal structure of CYP199A4 in complex with 2-naphthoic acid

Method: X-RAY DIFFRACTION Dmax: 95.0 Å Quality: EXCELLENT

1. Protein Identity and Related Structures Protein Identity & Related Structures

Cytochrome P450

Rhodopseudomonas palustris

UniProt Q2IU02

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 1–410 Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 1 FIV naphthalene-2-carboxylic acid × 2 SO4 SULFATE ION × 2 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.5;293 K;0.1M Bis-tris, 1.45M (NH4)2SO4, 0.1M NaCl, 0.1M CoCl2, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.00 Å R-free 0.287
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1–410 Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 1 FIV naphthalene-2-carboxylic acid × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.5;293 K;0.1M Bis-tris, 1.45M (NH4)2SO4, 0.1M NaCl, 0.1M CoCl2, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.00 Å R-free 0.287

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.

98 other PDB entries and 117 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q2IU02_RHOP2
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–410; UniProt 1–410 Author chain B; PDBConstruct 1–410; UniProt 1–410

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 4egp

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4egp
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id4egp
Deposition date deposition_date2012-03-31
Structure title titleThe X-ray crystal structure of CYP199A4 in complex with 2-naphthoic acid
Keywords keywordsCytochrome P450, Secondary metabolites biosynthesis, transport, catabolism, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier30.40
Radius of gyration Rg (electron density) rg_electron29.66
Forward intensity I(0) i0123043000.00
Molecular weight molecular_weight87849.0 kDa
Excluded volume excluded_volume109860 ų
Envelope volume envelope_volume132990 ų
Hydration-shell volume shell_volume36763 ų
Envelope diameter envelope_diameter93.5
Shell Rg shell_rg37.62
Envelope Rg envelope_rg29.51
Shape Rg shape_rg29.68
Total Rg total_rg30.27
Total atoms total_atoms6189
Residues n_residues786
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 dmax95.0
Rg (real space) rg_real30.35
Rg uncertainty (real space) rg_real_error0.56
I(0) (real space) i0_real1.2300e+08
I(0) uncertainty (real space) i0_real_error1.7550e+06
Rg (reciprocal space) rg_reciprocal30.37
I(0) (reciprocal space) i0_reciprocal123000000.0000
Solution quality estimate total_estimate0.9076
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.9
Skewness Skewness skewness0.239
Kurtosis Kurtosis kurtosis-0.641
Angular range angular_range— – 0.2600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha31830000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.947; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.958

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_idd4egpa_
Class classa — All alpha proteins
Fold Fold folda.104 — Cytochrome P450
Superfamily Superfamily superfamilya.104.1 — Cytochrome P450
Family Family familya.104.1.0 — automated matches
Domain ID domain_idd4egpb_
Class classa — All alpha proteins
Fold Fold folda.104 — Cytochrome P450
Superfamily Superfamily superfamilya.104.1 — Cytochrome P450
Family Family familya.104.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id4egpA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450
Domain ID domain_id4egpB00
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)