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Yorodumi- PDB-1wyu: Crystal structure of glycine decarboxylase (P-protein) of the gly... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wyu | ||||||
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Title | Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in holo form | ||||||
Components |
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Keywords | OXIDOREDUCTASE / ALPHA(2)BETA(2) TETRAMER / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Function and homology information glycine dehydrogenase (aminomethyl-transferring) / glycine dehydrogenase (decarboxylating) activity / glycine decarboxylation via glycine cleavage system / nucleoside metabolic process Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2.1 Å | ||||||
Authors | Nakai, T. / Nakagawa, N. / Maoka, N. / Masui, R. / Kuramitsu, S. / Kamiya, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Embo J. / Year: 2005 Title: Structure of P-protein of the glycine cleavage system: implications for nonketotic hyperglycinemia Authors: Nakai, T. / Nakagawa, N. / Maoka, N. / Masui, R. / Kuramitsu, S. / Kamiya, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wyu.cif.gz | 725.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wyu.ent.gz | 609.1 KB | Display | PDB format |
PDBx/mmJSON format | 1wyu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wy/1wyu ftp://data.pdbj.org/pub/pdb/validation_reports/wy/1wyu | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological assembly is an alpha(2)beta(2) tetramer. The asymmetric unit contains two sets of the assembly (chains A-D and E-H). |
-Components
#1: Protein | Mass: 47168.133 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: GCSA / Plasmid: pET11A / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3) References: UniProt: Q5SKW8, glycine dehydrogenase (aminomethyl-transferring) #2: Protein | Mass: 52784.711 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: GCSB / Plasmid: pET11A / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3) References: UniProt: Q5SKW7, glycine dehydrogenase (aminomethyl-transferring) #3: Chemical | ChemComp-PLP / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 3350, lithium sulfate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 12, 2004 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 247974 / Num. obs: 245553 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.673 / Mean I/σ(I) obs: 2.6 / Num. unique all: 23611 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: SIR / Resolution: 2.1→49.57 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 5117704.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.5308 Å2 / ksol: 0.349316 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→49.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
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Xplor file |
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