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Yorodumi- PDB-5z0y: Crystallization and structure determination of cytoplasm serine h... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5z0y | ||||||
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Title | Crystallization and structure determination of cytoplasm serine hydroxymethyltransferase (SHMT) from Pichia pastoris | ||||||
Components | Serine hydroxymethyltransferase | ||||||
Keywords | TRANSFERASE / SHMT / pichia pastoris / cytoplasm serine hydroxymethyltransferase | ||||||
Function / homology | Function and homology information glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / methyltransferase activity / pyridoxal phosphate binding / methylation Similarity search - Function | ||||||
Biological species | Komagataella phaffii (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Chen, Z. / Zhang, M. | ||||||
Funding support | China, 1items
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Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2018 Title: Structure and function of cytoplasmic serine hydroxymethyltransferase from Pichia pastoris Authors: Zhang, M. / Wu, W. / Chen, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5z0y.cif.gz | 87.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z0y.ent.gz | 63.4 KB | Display | PDB format |
PDBx/mmJSON format | 5z0y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5z0y_validation.pdf.gz | 443.1 KB | Display | wwPDB validaton report |
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Full document | 5z0y_full_validation.pdf.gz | 443.8 KB | Display | |
Data in XML | 5z0y_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 5z0y_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z0/5z0y ftp://data.pdbj.org/pub/pdb/validation_reports/z0/5z0y | HTTPS FTP |
-Related structure data
Related structure data | 1ls3S 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: 52151.238 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1) (fungus) Strain: ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1 Gene: SHM2, PP7435_Chr4-0570 / Production host: Komagataella pastoris (fungus) References: UniProt: F2QZA4, glycine hydroxymethyltransferase |
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#2: Chemical | ChemComp-GOL / |
#3: 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: 2.44 Å3/Da / Density % sol: 49.54 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / Details: 18% PEG8000, 0.1M MES pH 6.0, 0.2M Ca(OAc)2 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 8, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 17959 / % possible obs: 99.4 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 2.46 |
Reflection shell | Resolution: 2.5→2.54 Å / Rmerge(I) obs: 0.924 / Num. unique obs: 874 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LS3 Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / SU B: 14.529 / SU ML: 0.276 / Cross valid method: THROUGHOUT / ESU R: 0.415 / ESU R Free: 0.272 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.933 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→50 Å
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Refine LS restraints |
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