1m0q

Structure of Dialkylglycine Decarboxylase Complexed with S-1-aminoethanephosphonate

Method: X-RAY DIFFRACTION Dmax: 69.5 Å Quality: EXCELLENT

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

2,2-Dialkylglycine Decarboxylase

Burkholderia cepacia

UniProt P16932

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 1–433 Not recorded K POTASSIUM ION × 4 NA SODIUM ION × 4 EPC (1S)-1-[((1E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLENE)AMINO]ETHYLPHOSPHONIC ACID × 4 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.4;15% PEG 4000, 0.20 - 0.40 M SODIUM PYRUVATE, 0.015 M MES-KOH (pH 6.4) Resolution 2.00 Å R-free 0.240

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.

15 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DGDA_BURCE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–433; UniProt 1–433

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 1m0q

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1m0q
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1m0q
Deposition date deposition_date2002-06-13
Structure title titleStructure of Dialkylglycine Decarboxylase Complexed with S-1-aminoethanephosphonate
Keywords keywordsDecarboxylase, Pyridoxal phosphate, Lyase; LYASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier23.14
Radius of gyration Rg (electron density) rg_electron21.99
Forward intensity I(0) i036848300.00
Molecular weight molecular_weight46717.0 kDa
Excluded volume excluded_volume58485 ų
Envelope volume envelope_volume68826 ų
Hydration-shell volume shell_volume25767 ų
Envelope diameter envelope_diameter71.5
Shell Rg shell_rg29.21
Envelope Rg envelope_rg22.11
Shape Rg shape_rg22.01
Total Rg total_rg22.77
Total atoms total_atoms3276
Residues n_residues431
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 dmax69.5
Rg (real space) rg_real23.01
Rg uncertainty (real space) rg_real_error0.28
I(0) (real space) i0_real3.6850e+07
I(0) uncertainty (real space) i0_real_error4.4720e+05
Rg (reciprocal space) rg_reciprocal23.04
I(0) (reciprocal space) i0_reciprocal36850000.0000
Solution quality estimate total_estimate0.9124
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.8
Skewness Skewness skewness0.160
Kurtosis Kurtosis kurtosis-0.496
Angular range angular_range— – 0.3450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5194000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.959; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.990

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1m0qa_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamilyc.67.1 — PLP-dependent transferases
Family Family familyc.67.1.4 — GABA-aminotransferase-like

CATH v4.4 (2 domains)

Domain ID domain_id1m0qA01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily10 — Aspartate Aminotransferase, domain 1
Domain ID domain_id1m0qA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

8. Citations (1)

9. Files and Curves (10)