5kdb

The crystal structure of 4-isopropylbenzoate-bound CYP199A4

Method: X-RAY DIFFRACTION Dmax: 66.0 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 18–410 Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 1 4IA 4-propan-2-ylbenzoic acid × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.5;289.15 K;0.2M Magnesium acetate PEG 3350 - 23% w/v 0.1M Bis-Tris, pH 5.5 Resolution 1.64 Å R-free 0.186

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 1–393; UniProt 18–410

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 5kdb

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id5kdb
Deposition date deposition_date2016-06-07
Structure title titleThe crystal structure of 4-isopropylbenzoate-bound CYP199A4
Keywords keywordsP450, Oxidoreductase, Substrate; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier21.48
Radius of gyration Rg (electron density) rg_electron20.33
Forward intensity I(0) i031790300.00
Molecular weight molecular_weight43658.0 kDa
Excluded volume excluded_volume54682 ų
Envelope volume envelope_volume60760 ų
Hydration-shell volume shell_volume24331 ų
Envelope diameter envelope_diameter68.9
Shell Rg shell_rg27.50
Envelope Rg envelope_rg20.52
Shape Rg shape_rg20.31
Total Rg total_rg21.25
Total atoms total_atoms6112
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_real21.33
Rg uncertainty (real space) rg_real_error0.32
I(0) (real space) i0_real3.1790e+07
I(0) uncertainty (real space) i0_real_error3.9670e+05
Rg (reciprocal space) rg_reciprocal21.36
I(0) (reciprocal space) i0_reciprocal31790000.0000
Solution quality estimate total_estimate0.9035
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.2
Skewness Skewness skewness0.134
Kurtosis Kurtosis kurtosis-0.485
Angular range angular_range— – 0.3700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6649000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.986

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_idd5kdba_
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_id5kdbA00
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)