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Yorodumi- PDB-1d7r: CRYSTAL STRUCTURE OF THE COMPLEX OF 2,2-DIALKYLGLYCINE DECARBOXYL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d7r | ||||||
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Title | CRYSTAL STRUCTURE OF THE COMPLEX OF 2,2-DIALKYLGLYCINE DECARBOXYLASE WITH 5PA | ||||||
Components | PROTEIN (2,2-DIALKYLGLYCINE DECARBOXYLASE (PYRUVATE)) | ||||||
Keywords | LYASE / ENZYME COMPLEXES / CATALYTIC MECHANISM / DECARBOXYLATION INHIBITOR | ||||||
Function / homology | Function and homology information 2,2-dialkylglycine decarboxylase (pyruvate) / 2,2-dialkylglycine decarboxylase (pyruvate) activity / L-alanine catabolic process, by transamination / alanine-glyoxylate transaminase activity / glyoxylate catabolic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Burkholderia cepacia (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Malashkevich, V.N. / Toney, M.D. / Strop, P. / Keller, J. / Jansonius, J.N. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Crystal structures of dialkylglycine decarboxylase inhibitor complexes. Authors: Malashkevich, V.N. / Strop, P. / Keller, J.W. / Jansonius, J.N. / Toney, M.D. #1: Journal: J.Mol.Biol. / Year: 1991 Title: Crystallization and Preliminary X-Ray Diffraction Studies of Dialkylglycine Decarboxylase, a Decarboxylating Transaminase Authors: Toney, M.D. / Keller, J.W. / Pauptit, R.A. / Jaeger, J. / Wise, M.K. / Sauder, U. / Jansonius, J.N. #2: Journal: J.Biol.Chem. / Year: 1990 Title: Pseudomonas cepacia 2,2-Dialkylglycine Decarboxylase. Sequence and Expression in Escherichia Coli of Structural and Repressor Genes Authors: Keller, J.W. / Baurick, K.B. / Rutt, G.C. / O'Malley, M.V. / Sonafrank, N.L. / Reynolds, R.A. / Ebbesson, L.O. / Vajdos, F.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d7r.cif.gz | 98.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d7r.ent.gz | 73.6 KB | Display | PDB format |
PDBx/mmJSON format | 1d7r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d7r_validation.pdf.gz | 454 KB | Display | wwPDB validaton report |
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Full document | 1d7r_full_validation.pdf.gz | 465.8 KB | Display | |
Data in XML | 1d7r_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 1d7r_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/1d7r ftp://data.pdbj.org/pub/pdb/validation_reports/d7/1d7r | HTTPS FTP |
-Related structure data
Related structure data | 1d7sC 1d7uC 1d7vC 2dkbS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 46495.320 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia cepacia (bacteria) / Plasmid: PKDHE19 / Production host: Escherichia coli (E. coli) / Strain (production host): TY103 References: UniProt: P16932, 2,2-dialkylglycine decarboxylase (pyruvate) |
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#2: Chemical | ChemComp-NA / |
#3: Chemical | ChemComp-K / |
#4: Chemical | ChemComp-5PA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 61 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 15% PEG 4000, 0.15 M SODIUM PYRUVATE, 0.03 M MES-KOH, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: 4 micro litter of drop was mixed with 2 micro litter reservoir | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 26, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2→35 Å / Num. obs: 42301 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 25.83 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.318 / % possible all: 96.4 |
Reflection shell | *PLUS % possible obs: 96.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DKB Resolution: 2→10 Å / Isotropic thermal model: RESTRAINED / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 155.3 Å2 / ksol: 0.67 e/Å3 | ||||||||||||
Displacement parameters | Biso mean: 33.34 Å2 | ||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.27 Å | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||
Refine LS restraints | *PLUS Type: t_plane_restr / Dev ideal: 0.011 |