1pt0

Unprocessed Pyruvoyl Dependent Aspartate Decarboxylase with an Alanine insertion at position 26

Method: X-RAY DIFFRACTION Dmax: 60.6 Å Quality: EXCELLENT

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

Aspartate 1-decarboxylase

Escherichia coli

UniProt P0A790

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 1–126 Chain B; UniProt 1–126 Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4;290 K;1.4-1.6M Ammonium Sulphate, 0.1M Citric Acid, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K Resolution 2.00 Å R-free 0.191

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.

17 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PAND_ECOLI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 18–144; UniProt 1–126 Author chain B; PDBConstruct 18–144; UniProt 1–126

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 1pt0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1pt0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1pt0
Deposition date deposition_date2003-06-22
Structure title titleUnprocessed Pyruvoyl Dependent Aspartate Decarboxylase with an Alanine insertion at position 26
Keywords keywordsDecarboxylase, Pantothenate pathway, Protein Self-Processing, LYASE; LYASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier19.54
Radius of gyration Rg (electron density) rg_electron18.41
Forward intensity I(0) i012153700.00
Molecular weight molecular_weight24922.0 kDa
Excluded volume excluded_volume30684 ų
Envelope volume envelope_volume35575 ų
Hydration-shell volume shell_volume16544 ų
Envelope diameter envelope_diameter60.9
Shell Rg shell_rg23.92
Envelope Rg envelope_rg18.62
Shape Rg shape_rg18.41
Total Rg total_rg19.22
Total atoms total_atoms1748
Residues n_residues233
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 dmax60.6
Rg (real space) rg_real19.47
Rg uncertainty (real space) rg_real_error0.37
I(0) (real space) i0_real1.2150e+07
I(0) uncertainty (real space) i0_real_error1.6380e+05
Rg (reciprocal space) rg_reciprocal19.48
I(0) (reciprocal space) i0_reciprocal12150000.0000
Solution quality estimate total_estimate0.9117
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.1
Skewness Skewness skewness0.213
Kurtosis Kurtosis kurtosis-0.523
Angular range angular_range— – 0.4050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1721000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.957; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.978

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1pt0a1
Class classb — All beta proteins
Fold Fold foldb.52 — Double psi beta-barrel
Superfamily Superfamily superfamilyb.52.2 — ADC-like
Family Family familyb.52.2.1 — Pyruvoyl dependent aspartate decarboxylase, ADC
Domain ID domain_idd1pt0a2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1pt0b_
Class classb — All beta proteins
Fold Fold foldb.52 — Double psi beta-barrel
Superfamily Superfamily superfamilyb.52.2 — ADC-like
Family Family familyb.52.2.1 — Pyruvoyl dependent aspartate decarboxylase, ADC

CATH v4.4 (2 domains)

Domain ID domain_id1pt0A00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily20
Domain ID domain_id1pt0B00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily20

8. Citations (4)

9. Files and Curves (10)