6pqd

The crystal structure of 3-methylthiobenzoate-bound CYP199A4

Method: X-RAY DIFFRACTION Dmax: 65.8 Å Quality: EXCELLENT

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

Cytochrome P450

Rhodopseudomonas palustris (strain HaA2)

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 OVP 3-(methylsulfanyl)benzoic acid × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;289 K;1:1 35-40 mg/mL CYP199A4 (in 50 mM Tris-HCl, pH 7.4) + reservoir (0.2 M magnesium acetate, 100 mM Bis-Tris buffer adjusted with acetic acid to pH 5.0-5.75, 20-32% w/v PEG3350) Resolution 1.89 Å R-free 0.200

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 118 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

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 6pqd

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6pqd
Deposition date deposition_date2019-07-09
Structure title titleThe crystal structure of 3-methylthiobenzoate-bound CYP199A4
Keywords keywordsCytochrome P450, 3-methylthiobenzoic acid, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier21.42
Radius of gyration Rg (electron density) rg_electron20.29
Forward intensity I(0) i032041100.00
Molecular weight molecular_weight43662.0 kDa
Excluded volume excluded_volume54649 ų
Envelope volume envelope_volume60611 ų
Hydration-shell volume shell_volume24303 ų
Envelope diameter envelope_diameter68.6
Shell Rg shell_rg27.44
Envelope Rg envelope_rg20.49
Shape Rg shape_rg20.27
Total Rg total_rg21.21
Total atoms total_atoms3076
Residues n_residues393
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 dmax65.8
Rg (real space) rg_real21.27
Rg uncertainty (real space) rg_real_error0.31
I(0) (real space) i0_real3.2040e+07
I(0) uncertainty (real space) i0_real_error3.6820e+05
Rg (reciprocal space) rg_reciprocal21.30
I(0) (reciprocal space) i0_reciprocal32040000.0000
Solution quality estimate total_estimate0.9027
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.1
Skewness Skewness skewness0.137
Kurtosis Kurtosis kurtosis-0.484
Angular range angular_range— – 0.3700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6896000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.923; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.975

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd6pqda_
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 (1 domains)

Domain ID domain_id6pqdA00
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)