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Yorodumi- PDB-1wyv: Crystal structure of glycine decarboxylase (P-protein) of the gly... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wyv | ||||||
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Title | Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in inhibitor-bound 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 cleavage complex / glycine decarboxylation via glycine cleavage system / nucleoside metabolic process / glycine binding / pyridoxal phosphate binding / cytosol Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 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 | 1wyv.cif.gz | 710.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wyv.ent.gz | 580.3 KB | Display | PDB format |
PDBx/mmJSON format | 1wyv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wyv_validation.pdf.gz | 524.1 KB | Display | wwPDB validaton report |
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Full document | 1wyv_full_validation.pdf.gz | 596.7 KB | Display | |
Data in XML | 1wyv_validation.xml.gz | 138.9 KB | Display | |
Data in CIF | 1wyv_validation.cif.gz | 193.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wy/1wyv ftp://data.pdbj.org/pub/pdb/validation_reports/wy/1wyv | HTTPS FTP |
-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: GenBank: 55771907, UniProt: Q5SKW8*PLUS, 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: GenBank: 55771908, UniProt: Q5SKW7*PLUS, glycine dehydrogenase (aminomethyl-transferring) #3: Chemical | ChemComp-PLP / #4: Chemical | ChemComp-AOA / ( #5: 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: BL44B2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 29, 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: 2.4→50 Å / Num. all: 167358 / Num. obs: 166371 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 3.1 / Num. unique all: 16003 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: P-PROTEIN IN THE HOLO-FORM Resolution: 2.4→47.9 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 4234196.18 / 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: 36.302 Å2 / ksol: 0.353867 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→47.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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