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- PDB-1m0n: Structure of Dialkylglycine Decarboxylase Complexed with 1-Aminoc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1m0n | ||||||
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Title | Structure of Dialkylglycine Decarboxylase Complexed with 1-Aminocyclopentanephosphonate | ||||||
![]() | 2,2-Dialkylglycine decarboxylase | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Liu, W. / Rogers, C.J. / Fisher, A.J. / Toney, M.D. | ||||||
![]() | ![]() Title: Aminophosphonate Inhibitors of Dialkylglycine Decarboxylase: Structural Basis for Slow Binding Inhibition Authors: Liu, W. / Rogers, C.J. / Fisher, A.J. / Toney, M.D. | ||||||
History |
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Remark 999 | SEQUENCE AUTHORS STATE THAT RESIDUES GLN 15 AND GLY 81 FROM THE SWISSPROT ENTRY ARE INCORRECT. ...SEQUENCE AUTHORS STATE THAT RESIDUES GLN 15 AND GLY 81 FROM THE SWISSPROT ENTRY ARE INCORRECT. THESE RESIDUES SHOULD BE HIS 15 AND GLU 81. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 100.3 KB | Display | ![]() |
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PDB format | ![]() | 75.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1m0oC ![]() 1m0pC ![]() 1m0qC ![]() 1dkaS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 46577.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P16932, ![]() |
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#2: Chemical | ChemComp-K / |
#3: Chemical | ChemComp-NA / |
#4: Chemical | ChemComp-HCP / |
#5: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 61 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | pH: 6.4 Details: 15% PEG 4000, 0.2-0.4 M SODIUM PYRUVATE, 0.015 M MES-KOH (PH 6.4) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.2→30 Å / Num. obs: 28332 / % possible obs: 96.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -2 / Redundancy: 3.21 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 2→2.28 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 11.3 / % possible all: 98.1 |
Reflection | *PLUS Lowest resolution: 20 Å / Rmerge(I) obs: 0.077 |
Reflection shell | *PLUS Rmerge(I) obs: 0.318 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1DKA Resolution: 2.2→20 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 211 Å2 / ksol: 0.78 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.192 / Rfactor Rfree![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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