4azd

T57V mutant of aspartate decarboxylase

Method: X-RAY DIFFRACTION Dmax: 67.4 Å Quality: GOOD

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 Mutation:YES MLI MALONATE ION × 8 X-RAY DIFFRACTION X-ray crystallization conditions:pH 4;292 K;2.4 M SODIUM MALONATE, 1.5 M (NH4)2SO4 PH 4, 292 K Resolution 1.62 Å R-free 0.217

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 18–143; UniProt 1–126 Author chain B; PDBConstruct 18–143; 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 4azd

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4azd
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4azd
Deposition date deposition_date2012-06-25
Structure title titleT57V mutant of aspartate decarboxylase
Keywords keywordsLYASE, AMINO ACID SUBSTITUTION; LYASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier19.88
Radius of gyration Rg (electron density) rg_electron18.73
Forward intensity I(0) i013543400.00
Molecular weight molecular_weight26506.0 kDa
Excluded volume excluded_volume32696 ų
Envelope volume envelope_volume38579 ų
Hydration-shell volume shell_volume17458 ų
Envelope diameter envelope_diameter66.9
Shell Rg shell_rg24.74
Envelope Rg envelope_rg19.16
Shape Rg shape_rg18.71
Total Rg total_rg19.63
Total atoms total_atoms1861
Residues n_residues239
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 dmax67.4
Rg (real space) rg_real19.82
Rg uncertainty (real space) rg_real_error0.43
I(0) (real space) i0_real1.3540e+07
I(0) uncertainty (real space) i0_real_error1.6670e+05
Rg (reciprocal space) rg_reciprocal19.83
I(0) (reciprocal space) i0_reciprocal13540000.0000
Solution quality estimate total_estimate0.8838
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.8
Skewness Skewness skewness0.237
Kurtosis Kurtosis kurtosis-0.472
Angular range angular_range— – 0.4000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2202000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.842; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.991

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_idd4azda1
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_idd4azda2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4azdb_
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_id4azdA00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily20
Domain ID domain_id4azdB00
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)