3tm7

Processed Aspartate Decarboxylase Mutant with Asn72 mutated to Ala

Method: X-RAY DIFFRACTION Dmax: 82.2 Å Quality: GOOD

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

Aspartate 1-decarboxylase beta chain

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 × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain A; UniProt 1–24 Chain B; UniProt 25–126 Chain C; UniProt 1–24 Chain D; UniProt 25–126 Mutation:N72A SO4 SULFATE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4;298 K;1.6-2.4M ammonium sulphate, 0.1M citric acid, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K Resolution 1.70 Å R-free 0.184
2 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 1–24 Chain B; UniProt 25–126 Chain C; UniProt 1–24 Chain D; UniProt 25–126 Mutation:N72A SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4;298 K;1.6-2.4M ammonium sulphate, 0.1M citric acid, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K Resolution 1.70 Å R-free 0.184

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 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PAND_ECOLI
Isoform
PDB entities 1, 2
Chains and sequence ranges Author chain A; PDBConstruct 3–26; UniProt 1–24 Author chain C; PDBConstruct 3–26; UniProt 1–24 Author chain B; PDBConstruct 1–102; UniProt 25–126 Author chain D; PDBConstruct 1–102; UniProt 25–126

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 3tm7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3tm7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3tm7
Deposition date deposition_date2011-08-31
Structure title titleProcessed Aspartate Decarboxylase Mutant with Asn72 mutated to Ala
Keywords keywordsAUTO-PROCESSING, LYASE, Pyruvoyl; LYASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier20.12
Radius of gyration Rg (electron density) rg_electron19.30
Forward intensity I(0) i013072400.00
Molecular weight molecular_weight26002.0 kDa
Excluded volume excluded_volume32089 ų
Envelope volume envelope_volume38753 ų
Hydration-shell volume shell_volume17252 ų
Envelope diameter envelope_diameter84.5
Shell Rg shell_rg25.05
Envelope Rg envelope_rg20.56
Shape Rg shape_rg19.30
Total Rg total_rg20.13
Total atoms total_atoms1822
Residues n_residues244
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 dmax82.2
Rg (real space) rg_real20.18
Rg uncertainty (real space) rg_real_error0.85
I(0) (real space) i0_real1.3070e+07
I(0) uncertainty (real space) i0_real_error2.0790e+05
Rg (reciprocal space) rg_reciprocal20.17
I(0) (reciprocal space) i0_reciprocal13070000.0000
Solution quality estimate total_estimate0.7681
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.3
Skewness Skewness skewness0.539
Kurtosis Kurtosis kurtosis0.454
Angular range angular_range— – 0.3950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2464000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.431; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.687; Smooth: 1.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id3tm7B00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily20
Domain ID domain_id3tm7D00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily20

8. Citations (1)

9. Files and Curves (10)