5fhq

Crystal structure of (WT) Rat Catechol-O-Methyltransferase in complex with AdoMet and 3,5-dinitrocatechol (DNC)

Method: X-RAY DIFFRACTION Dmax: 48.7 Å Quality: REASONABLE

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

Catechol O-methyltransferase

Rattus norvegicus

UniProt P22734

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 46–258 Not recorded SAM S-ADENOSYLMETHIONINE × 1 DNC 3,5-DINITROCATECHOL × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.4;277 K;200 nL of protein with an equal volume of reservoir solution comprising (0.09 M [0.2 M sodium formate; 0.2 M ammonium acetate; 0.2 M sodium citrate tribasic dihydrate; 0.2 M sodium potassium tartrate tetrahydrate; 0.2 M sodium oxamate] 0.1 M Tris / Bicine pH 8.5, 50% [40% v/v PEG 500* MME; 20 % w/v PEG 20000] Morpheus HT96 condition G9) Resolution 1.63 Å R-free 0.188

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.

96 other PDB entries and 160 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name COMT_RAT
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–213; UniProt 46–258

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 5fhq

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id5fhq
Deposition date deposition_date2015-12-22
Structure title titleCrystal structure of (WT) Rat Catechol-O-Methyltransferase in complex with AdoMet and 3,5-dinitrocatechol (DNC)
Keywords keywordsMethyltransferase Regioselectivity, transferase; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier19.08
Radius of gyration Rg (electron density) rg_electron18.74
Forward intensity I(0) i010876700.00
Molecular weight molecular_weight24558.0 kDa
Excluded volume excluded_volume30763 ų
Envelope volume envelope_volume37142 ų
Hydration-shell volume shell_volume17341 ų
Envelope diameter envelope_diameter83.3
Shell Rg shell_rg24.11
Envelope Rg envelope_rg20.96
Shape Rg shape_rg18.77
Total Rg total_rg19.47
Total atoms total_atoms3429
Residues n_residues213
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 dmax48.7
Rg (real space) rg_real17.38
Rg uncertainty (real space) rg_real_error0.05
I(0) (real space) i0_real1.0220e+07
I(0) uncertainty (real space) i0_real_error8.5690e+04
Rg (reciprocal space) rg_reciprocal19.32
I(0) (reciprocal space) i0_reciprocal10880000.0000
Solution quality estimate total_estimate0.6814
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary21.6
Skewness Skewness skewness0.192
Kurtosis Kurtosis kurtosis-0.367
Angular range angular_range— – 0.4150 −1
Current regularization parameter α current_alpha2.6060
Highest regularization parameter α highest_alpha2305000.0000
Real-space data points n_real_points73
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.014; Oscil: 0.978; Stabil: 0.980; Sysdev: 0.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.000

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_idd5fhqa_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamilyc.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family familyc.66.1.1 — COMT-like

CATH v4.4 (1 domains)

Domain ID domain_id5fhqA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily150 — Vaccinia Virus protein VP39

8. Citations (1)

9. Files and Curves (10)