1c4k

ORNITHINE DECARBOXYLASE MUTANT (GLY121TYR)

Method: X-RAY DIFFRACTION Dmax: 101.8 Å Quality: GOOD

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

PROTEIN (ORNITHINE DECARBOXYLASE)

Lactobacillus sp. 30A

UniProt P43099

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 1–730 Mutation:G121Y PLP PYRIDOXAL-5'-PHOSPHATE × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7;20 DEG, SITTING DROP, MICROBRIDGES, RESERVOIRS CONTAINING 30% PEG3350, 0.2 M AMMONIUM ACETATE, AND 0.1 M SODIUM HEPES PH 7.0. DROPS CONSISTED OF EQUAL VOLUMES RESERVOIR AND 20 MG/ML PROTEIN SOLUTION. Resolution 2.70 Å R-free 0.281
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–730 Mutation:G121Y PLP PYRIDOXAL-5'-PHOSPHATE × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7;20 DEG, SITTING DROP, MICROBRIDGES, RESERVOIRS CONTAINING 30% PEG3350, 0.2 M AMMONIUM ACETATE, AND 0.1 M SODIUM HEPES PH 7.0. DROPS CONSISTED OF EQUAL VOLUMES RESERVOIR AND 20 MG/ML PROTEIN SOLUTION. Resolution 2.70 Å R-free 0.281

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.

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DCOR_LACS3
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–730; UniProt 1–730

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 1c4k

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1c4k
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id1c4k
Deposition date deposition_date1999-08-26
Structure title titleORNITHINE DECARBOXYLASE MUTANT (GLY121TYR)
Keywords keywordsDECARBOXYLASE, ORNITHINE, LYASE; LYASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier29.95
Radius of gyration Rg (electron density) rg_electron28.97
Forward intensity I(0) i0111157000.00
Molecular weight molecular_weight83113.0 kDa
Excluded volume excluded_volume103730 ų
Envelope volume envelope_volume130500 ų
Hydration-shell volume shell_volume37186 ų
Envelope diameter envelope_diameter107.3
Shell Rg shell_rg36.40
Envelope Rg envelope_rg29.40
Shape Rg shape_rg28.96
Total Rg total_rg29.69
Total atoms total_atoms5872
Residues n_residues728
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 dmax101.8
Rg (real space) rg_real29.88
Rg uncertainty (real space) rg_real_error0.82
I(0) (real space) i0_real1.1120e+08
I(0) uncertainty (real space) i0_real_error1.6880e+06
Rg (reciprocal space) rg_reciprocal29.91
I(0) (reciprocal space) i0_reciprocal111200000.0000
Solution quality estimate total_estimate0.8785
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary38.4
Skewness Skewness skewness0.276
Kurtosis Kurtosis kurtosis-0.252
Angular range angular_range— – 0.2650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha22560000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.817; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.970

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1c4ka1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.1 — CheY-like
Family Family familyc.23.1.4 — Ornithine decarboxylase N-terminal 'wing' domain
Domain ID domain_idd1c4ka2
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.67.1.5 — Ornithine decarboxylase major domain
Domain ID domain_idd1c4ka3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.125 — Ornithine decarboxylase C-terminal domain
Superfamily Superfamily superfamilyd.125.1 — Ornithine decarboxylase C-terminal domain
Family Family familyd.125.1.1 — Ornithine decarboxylase C-terminal domain

CATH v4.4 (4 domains)

Domain ID domain_id1c4kA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily220
Domain ID domain_id1c4kA02
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)
Domain ID domain_id1c4kA03
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_id1c4kA04
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology100 — Ornithine Decarboxylase; Chain A, domain 4
Homologous superfamily homologous superfamily10 — Orn/Lys/Arg decarboxylase, C-terminal domain

8. Citations (1)

9. Files and Curves (10)