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1ord

CRYSTALLOGRAPHIC STRUCTURE OF A PLP-DEPENDENT ORNITHINE DECARBOXYLASE FROM LACTOBACILLUS 30A TO 3.1 ANGSTROMS RESOLUTION

Method: X-RAY DIFFRACTION Dmax: 106.3 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

ORNITHINE DECARBOXYLASE

OrganismNot specified

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 Chain B； UniProt 1–730 Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.00 Å R-free 0.268
2 Protein homooligomer Homooligomer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count Chain A； UniProt 1–730 Chain B； UniProt 1–730 Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 12 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.00 Å R-free 0.268

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.

Other PDB Difference from Current Entry 1ORD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1C4K ORNITHINE DECARBOXYLASE MUTANT (GLY121TYR) Deposited 1999-08-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–730（730 aa）
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
1C4K ORNITHINE DECARBOXYLASE MUTANT (GLY121TYR) Deposited 1999-08-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–730（730 aa）
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

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 Author chain B； 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 1ord

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1ord
Deposition date deposition_date1995-02-08
Structure title titleCRYSTALLOGRAPHIC STRUCTURE OF A PLP-DEPENDENT ORNITHINE DECARBOXYLASE FROM LACTOBACILLUS 30A TO 3.1 ANGSTROMS RESOLUTION
Keywords keywordsCARBOXY-LYASE; CARBOXY-LYASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier34.61 Å
Radius of gyration Rg (electron density) rg_electron33.70 Å
Forward intensity I(0) i0413666000.00
Molecular weight molecular_weight165520.0 kDa
Excluded volume excluded_volume206990 ų
Envelope volume envelope_volume246870 ų
Hydration-shell volume shell_volume58155 ų
Envelope diameter envelope_diameter110.4 Å
Shell Rg shell_rg42.61 Å
Envelope Rg envelope_rg34.05 Å
Shape Rg shape_rg33.69 Å
Total Rg total_rg34.34 Å
Total atoms total_atoms14240
Residues n_residues1460
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax106.3 Å
Rg (real space) rg_real34.44 Å
Rg uncertainty (real space) rg_real_error0.63 Å
I(0) (real space) i0_real4.1370e+08
I(0) uncertainty (real space) i0_real_error6.8670e+06
Rg (reciprocal space) rg_reciprocal34.55 Å
I(0) (reciprocal space) i0_reciprocal413700000.0000
Solution quality estimate total_estimate0.9023
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary43.9 Å
Skewness Skewness skewness0.148
Kurtosis Kurtosis kurtosis-0.534
Angular range angular_range— – 0.2300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha106800000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.940; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.924
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd1orda1
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_idd1orda2
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_idd1orda3
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
Domain ID domain_idd1ordb1
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_idd1ordb2
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_idd1ordb3
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 (8 domains)

Domain ID domain_id1ordA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily220 —
Domain ID domain_id1ordA02
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_id1ordA03
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_id1ordA04
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
Domain ID domain_id1ordB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily220 —
Domain ID domain_id1ordB02
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_id1ordB03
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_id1ordB04
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
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8. Citations (2)

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9. Files and Curves (10)