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Yorodumi- PDB-2zr8: Crystal Structure of Modified Serine Racemase complexed with Serine -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zr8 | ||||||
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Title | Crystal Structure of Modified Serine Racemase complexed with Serine | ||||||
Components | Uncharacterized protein C320.14 | ||||||
Keywords | ISOMERASE / PLP-dependent / Lyase / Pyridoxal phosphate | ||||||
Function / homology | Function and homology information Serine biosynthesis / serine racemase / threonine racemase activity / serine racemase activity / D-serine ammonia-lyase / D-serine ammonia-lyase activity / L-serine ammonia-lyase / L-serine ammonia-lyase activity / D-serine metabolic process / L-serine metabolic process ...Serine biosynthesis / serine racemase / threonine racemase activity / serine racemase activity / D-serine ammonia-lyase / D-serine ammonia-lyase activity / L-serine ammonia-lyase / L-serine ammonia-lyase activity / D-serine metabolic process / L-serine metabolic process / pyridoxal phosphate binding / magnesium ion binding / protein homodimerization activity / ATP binding Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Goto, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Crystal structure of a homolog of mammalian serine racemase from Schizosaccharomyces pombe Authors: Goto, M. / Yamauchi, T. / Kamiya, N. / Miyahara, I. / Yoshimura, T. / Mihara, H. / Kurihara, T. / Hirotsu, K. / Esaki, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zr8.cif.gz | 77 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zr8.ent.gz | 56.1 KB | Display | PDB format |
PDBx/mmJSON format | 2zr8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zr/2zr8 ftp://data.pdbj.org/pub/pdb/validation_reports/zr/2zr8 | HTTPS FTP |
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-Related structure data
Related structure data | 1wtcC 2zpuS S: Starting model for refinement C: citing same article (ref.) |
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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: 35093.184 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: O59791, serine racemase |
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#2: Chemical | ChemComp-PDD / |
#3: Chemical | ChemComp-SER / |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
Nonpolymer details | SER A 370 WORKS AS SUBSTRATE. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 21% PEG 4000, 0.2M Magnesium Acetate, 10% MPD, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 19, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→99 Å / Num. all: 13852 / Num. obs: 13720 / % possible obs: 99.2 % / Biso Wilson estimate: 13.6 Å2 |
Reflection shell | Resolution: 2.2→2.26 Å / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZPU Resolution: 2.2→19.57 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1531848.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.5468 Å2 / ksol: 0.400967 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→19.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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