4d7z

E. coli L-aspartate-alpha-decarboxylase mutant N72Q to a resolution of 1.9 Angstroms

Method: X-RAY DIFFRACTION Dmax: 60.6 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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–24 Chain B; UniProt 25–119 Fragment:RESIDUES 25-119 Mutation:YES Non-standard monomer:Yes (specific site not provided by mmCIF) PEG DI(HYDROXYETHYL)ETHER × 1 SCN THIOCYANATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.8;ADC.PANZ COMPLEX WAS PREPARED IN A 10: 11 RATIO AT A FINAL CONCENTRATION OF 5.7 MG/ML WITH A 2-FOLD MOLAR EXCESS (RELATIVE TO PANZ) OF ACETYLCOA IN 0.05 M TRIS-HCL PH 7.69, 0.1 M NACL, 0.1 MM DTT. THIS WAS MIXED IN A 1:1 RATIO WITH RESERVOIR SOLUTION (0.2 M POTASSIUM THIOCYANATE, 0.1 M BIS- TRIS PROPANE PH 6.8, 20 % W/V PEG 3350) AND CRYSTALLIZED BY HANGING DROP VAOUR DIFFUSION (4 UL DROPLET OVER A 1 ML RESERVOIR). Resolution 1.90 Å R-free 0.244

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, 2
Chains and sequence ranges Author chain A; PDBConstruct 18–41; UniProt 1–24 Author chain B; PDBConstruct 1–95; UniProt 25–119

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 4d7z

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4d7z
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4d7z
Deposition date deposition_date2014-12-02
Structure title titleE. coli L-aspartate-alpha-decarboxylase mutant N72Q to a resolution of 1.9 Angstroms
Keywords keywordsLYASE, PROTEIN DERIVED COFACTOR, PANTOTHENATE SYNTHESIS, PYRUVOYL COFACTOR, BETA-ALANINE; LYASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier16.69
Radius of gyration Rg (electron density) rg_electron15.59
Forward intensity I(0) i04010250.00
Molecular weight molecular_weight13645.0 kDa
Excluded volume excluded_volume16846 ų
Envelope volume envelope_volume20023 ų
Hydration-shell volume shell_volume11631 ų
Envelope diameter envelope_diameter58.2
Shell Rg shell_rg20.56
Envelope Rg envelope_rg16.29
Shape Rg shape_rg15.55
Total Rg total_rg16.66
Total atoms total_atoms955
Residues n_residues122
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_real16.75
Rg uncertainty (real space) rg_real_error0.53
I(0) (real space) i0_real4.0100e+06
I(0) uncertainty (real space) i0_real_error5.2320e+04
Rg (reciprocal space) rg_reciprocal16.74
I(0) (reciprocal space) i0_reciprocal4010000.0000
Solution quality estimate total_estimate0.8281
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary19.7
Skewness Skewness skewness0.470
Kurtosis Kurtosis kurtosis-0.136
Angular range angular_range— – 0.4750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha642800.0000
Real-space data points n_real_points78
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.643; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.858; Smooth: 0.976

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id4d7zB00
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)