8vot

The crystal structure of wild-type CYP199A4 bound to 4-(hydroxymethyl)benzoic acid

Method: X-RAY DIFFRACTION Dmax: 66.0 Å Quality: REASONABLE

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

Cytochrome P450

Rhodopseudomonas palustris 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 E5X 4-(hydroxymethyl)benzoic acid × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CL CHLORIDE ION × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;289.15 K;The crystallization buffer was 100 mM Bis-Tris buffer (adjusted to pH 5.0-5.75 with acetic acid), 0.2 M magnesium acetate and 20-32% PEG 3350 Resolution 1.53 Å R-free 0.168

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 8vot

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8vot
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8vot
Deposition date deposition_date2024-01-16
Structure title titleThe crystal structure of wild-type CYP199A4 bound to 4-(hydroxymethyl)benzoic acid
Keywords keywordsCytochrome P450, catalytic product, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier21.50
Radius of gyration Rg (electron density) rg_electron20.34
Forward intensity I(0) i032100400.00
Molecular weight molecular_weight43695.0 kDa
Excluded volume excluded_volume54681 ų
Envelope volume envelope_volume60781 ų
Hydration-shell volume shell_volume24320 ų
Envelope diameter envelope_diameter68.5
Shell Rg shell_rg27.50
Envelope Rg envelope_rg20.54
Shape Rg shape_rg20.32
Total Rg total_rg21.28
Total atoms total_atoms3078
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 dmax66.0
Rg (real space) rg_real21.34
Rg uncertainty (real space) rg_real_error0.36
I(0) (real space) i0_real3.2100e+07
I(0) uncertainty (real space) i0_real_error4.3540e+05
Rg (reciprocal space) rg_reciprocal21.37
I(0) (reciprocal space) i0_reciprocal32100000.0000
Solution quality estimate total_estimate0.6931
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.2
Skewness Skewness skewness0.130
Kurtosis Kurtosis kurtosis-0.499
Angular range angular_range— – 0.3700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6915000.0000
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: 0.083; Positv: 1.000; Valcen: 0.989; Smooth: 0.997

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)