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1zod

Crystal structure of dialkylglycine decarboxylase bound with cesium ion

Method: X-RAY DIFFRACTION Dmax: 71.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

2,2-dialkylglycine decarboxylase

Burkholderia cepacia

UniProt P16932

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–432 Not recorded CS CESIUM ION × 1 NA SODIUM ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 PLP PYRIDOXAL-5'-PHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.4；298 K；PEG4K, MES, PLP, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.80 Å R-free 0.226
2 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1–432 Not recorded CS CESIUM ION × 4 NA SODIUM ION × 4 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 4 PLP PYRIDOXAL-5'-PHOSPHATE × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.4；298 K；PEG4K, MES, PLP, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.80 Å R-free 0.226

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 1ZOD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1D7R CRYSTAL STRUCTURE OF THE COMPLEX OF 2,2-DIALKYLGLYCINE DECARBOXYLASE WITH 5PA Deposited 1999-10-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–433（433 aa）
Not recorded NA SODIUM ION × 4 K POTASSIUM ION × 4 5PA N-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-Y-LMETHYL]-1-AMINO-CYCLOPROPANECARBOXYLIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；15% PEG 4000, 0.15 M SODIUM PYRUVATE, 0.03 M MES-KOH, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å
1D7S CRYSTAL STRUCTURE OF THE COMPLEX OF 2,2-DIALKYLGLYCINE DECARBOXYLASE WITH DCS Deposited 1999-10-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–433（433 aa）
Not recorded NA SODIUM ION × 4 K POTASSIUM ION × 4 DCS D-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；15% PEG 4000, 0.15 M SODIUM PYRUVATE, 0.03 M MES-KOH , pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.05 Å
1D7U Crystal structure of the complex of 2,2-dialkylglycine decarboxylase with LCS Deposited 1999-10-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–433（433 aa）
Not recorded NA SODIUM ION × 4 K POTASSIUM ION × 4 LCS [5-hydroxy-6-methyl-4-({[(4E)-3-oxo-1,2-oxazolidin-4-ylidene]amino}methyl)pyridin-3-yl]methyl dihydrogen phosphate × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；297 K；pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Resolution 1.95 Å
1D7V CRYSTAL STRUCTURE OF THE COMPLEX OF 2,2-DIALKYLGLYCINE DECARBOXYLASE WITH NMA Deposited 1999-10-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–433（433 aa）
Not recorded NA SODIUM ION × 4 K POTASSIUM ION × 4 NMA N-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-2-METHYLALANINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å
1DGD AN ALKALI METAL ION SIZE-DEPENDENT SWITCH IN THE ACTIVE SITE STRUCTURE OF DIALKYLGLYCINE DECARBOXYLASE Deposited 1994-06-29 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–432（432 aa）
Not recorded NA SODIUM ION × 4 LI LITHIUM ION × 4 PLP PYRIDOXAL-5'-PHOSPHATE × 4 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.80 Å
1DGE AN ALKALI METAL ION SIZE-DEPENDENT SWITCH IN THE ACTIVE SITE STRUCTURE OF DIALKYLGLYCINE DECARBOXYLASE Deposited 1994-06-29 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–432（432 aa）
Not recorded RB RUBIDIUM ION × 8 PLP PYRIDOXAL-5'-PHOSPHATE × 4 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.80 Å
1DGE AN ALKALI METAL ION SIZE-DEPENDENT SWITCH IN THE ACTIVE SITE STRUCTURE OF DIALKYLGLYCINE DECARBOXYLASE Deposited 1994-06-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–432（432 aa）
Not recorded RB RUBIDIUM ION × 4 PLP PYRIDOXAL-5'-PHOSPHATE × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.80 Å
1DKA DIALKYLGLYCINE DECARBOXYLASE STRUCTURE: BIFUNCTIONAL ACTIVE SITE AND ALKALI METAL BINDING SITES Deposited 1993-06-18 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–432（432 aa）
Not recorded NA SODIUM ION × 4 K POTASSIUM ION × 4 PLP PYRIDOXAL-5'-PHOSPHATE × 4 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.60 Å
1M0N Structure of Dialkylglycine Decarboxylase Complexed with 1-Aminocyclopentanephosphonate Deposited 2002-06-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–433（433 aa）
Not recorded K POTASSIUM ION × 4 NA SODIUM ION × 4 HCP 1-[((1E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLENE)AMINO]CYCLOPENTYLPHOSPHONIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.4；15% PEG 4000, 0.2-0.4 M SODIUM PYRUVATE, 0.015 M MES-KOH (PH 6.4)
Resolution 2.20 Å R-free 0.239
1M0O Structure of Dialkylglycine Decarboxylase Complexed with 1-Amino-1-methylpropanephosphonate Deposited 2002-06-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–433（433 aa）
Not recorded K POTASSIUM ION × 4 NA SODIUM ION × 4 MPM (1R)-1-[((1E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLENE)AMINO]-1-METHYLPROPYLPHOSPHONIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.4；15% PEG 4000, 0.20 - 0.40 M SODIUM PYRUVATE, 0.015 M MES-KOH (pH 6.4)
Resolution 2.40 Å R-free 0.201
1M0P Structure of Dialkylglycine Decarboxylase Complexed with 1-Amino-1-phenylethanephosphonate Deposited 2002-06-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–433（433 aa）
Not recorded K POTASSIUM ION × 4 NA SODIUM ION × 4 ELP (1R)-1-[((1E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLENE)AMINO]-1-PHENYLETHYLPHOSPHONIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.4；15% PEG 4000, 0.20 - 0.40 M SODIUM PYRUVATE, 0.015 M MES-KOH (pH 6.4)
Resolution 2.60 Å R-free 0.230
1M0Q Structure of Dialkylglycine Decarboxylase Complexed with S-1-aminoethanephosphonate Deposited 2002-06-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–433（433 aa）
Not recorded K POTASSIUM ION × 4 NA SODIUM ION × 4 EPC (1S)-1-[((1E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLENE)AMINO]ETHYLPHOSPHONIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.4；15% PEG 4000, 0.20 - 0.40 M SODIUM PYRUVATE, 0.015 M MES-KOH (pH 6.4)
Resolution 2.00 Å R-free 0.240
1Z3Z The crystal structure of a DGD mutant: Q52A Deposited 2005-03-14 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–432（431 aa）
Mutation：Q52A NA SODIUM ION × 1 K POTASSIUM ION × 1 PLP PYRIDOXAL-5'-PHOSPHATE × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；PEG4K, MES, PLP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.90 Å R-free 0.266
1ZC9 The crystal structure of dialkylglycine decarboxylase complex with pyridoxamine 5-phosphate Deposited 2005-04-11 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–432（432 aa）
Not recorded K POTASSIUM ION × 1 NA SODIUM ION × 1 PMP 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；298 K；MES, PEG4000, PLP, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.237
1ZOB Crystal structure of dialkylglycine decarboxylases bound with calcium ion Deposited 2005-05-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–432（432 aa）
Not recorded NA SODIUM ION × 1 CA CALCIUM ION × 1 PLP PYRIDOXAL-5'-PHOSPHATE × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；PEG4K, MES, PLP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.75 Å R-free 0.277
1ZOB Crystal structure of dialkylglycine decarboxylases bound with calcium ion Deposited 2005-05-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–432（432 aa）
Not recorded NA SODIUM ION × 4 CA CALCIUM ION × 4 PLP PYRIDOXAL-5'-PHOSPHATE × 4 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；PEG4K, MES, PLP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.75 Å R-free 0.277
2DKB DIALKYLGLYCINE DECARBOXYLASE STRUCTURE: BIFUNCTIONAL ACTIVE SITE AND ALKALI METAL BINDING SITES Deposited 1994-07-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–432（432 aa）
Not recorded NA SODIUM ION × 4 PLP PYRIDOXAL-5'-PHOSPHATE × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å
2DKB DIALKYLGLYCINE DECARBOXYLASE STRUCTURE: BIFUNCTIONAL ACTIVE SITE AND ALKALI METAL BINDING SITES Deposited 1994-07-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–432（432 aa）
Not recorded NA SODIUM ION × 8 PLP PYRIDOXAL-5'-PHOSPHATE × 4 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å

15 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DGDA_BURCE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–433； UniProt 1–432

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 1zod

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1zod
Deposition date deposition_date2005-05-12
Structure title titleCrystal structure of dialkylglycine decarboxylase bound with cesium ion
Keywords keywordsdecarboxylase, pyridoxal, cesium, LYASE; 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_guinier23.16 Å
Radius of gyration Rg (electron density) rg_electron21.98 Å
Forward intensity I(0) i037026500.00
Molecular weight molecular_weight46883.0 kDa
Excluded volume excluded_volume58691 ų
Envelope volume envelope_volume69311 ų
Hydration-shell volume shell_volume25890 ų
Envelope diameter envelope_diameter71.0 Å
Shell Rg shell_rg29.26 Å
Envelope Rg envelope_rg22.16 Å
Shape Rg shape_rg22.00 Å
Total Rg total_rg22.80 Å
Total atoms total_atoms3281
Residues n_residues431
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 dmax71.8 Å
Rg (real space) rg_real23.03 Å
Rg uncertainty (real space) rg_real_error0.42 Å
I(0) (real space) i0_real3.7030e+07
I(0) uncertainty (real space) i0_real_error5.1260e+05
Rg (reciprocal space) rg_reciprocal23.06 Å
I(0) (reciprocal space) i0_reciprocal37030000.0000
Solution quality estimate total_estimate0.7143
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.6 Å
Skewness Skewness skewness0.160
Kurtosis Kurtosis kurtosis-0.498
Angular range angular_range— – 0.3450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5434000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 0.171; Positv: 1.000; Valcen: 0.991; Smooth: 0.989
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1zoda_
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.67.1.4 — GABA-aminotransferase-like

CATH v4.4 (2 domains)

Domain ID domain_id1zodA01
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_id1zodA02
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)
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8. Citations (1)

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9. Files and Curves (10)