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Yorodumi- PDB-6ccz: Crystal structure of Medicago truncatula serine hydroxymethyltran... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ccz | ||||||
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Title | Crystal structure of Medicago truncatula serine hydroxymethyltransferase 3 (MtSHMT3) soaked with selenourea | ||||||
Components | (Serine hydroxymethyltransferase) x 2 | ||||||
Keywords | TRANSFERASE / PLP / one-carbon cycle / tetrahydrofolate / chloroplast / tetramer / SAD phasing | ||||||
Function / homology | Function and homology information serine binding / L-serine catabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / folic acid metabolic process / methyltransferase activity / pyridoxal phosphate binding ...serine binding / L-serine catabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / folic acid metabolic process / methyltransferase activity / pyridoxal phosphate binding / one-carbon metabolic process / methylation / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Medicago truncatula (barrel medic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.14 Å | ||||||
Authors | Ruszkowski, M. / Sekula, B. / Ruszkowska, A. / Dauter, Z. | ||||||
Citation | Journal: Front Plant Sci / Year: 2018 Title: Chloroplastic Serine Hydroxymethyltransferase FromMedicago truncatula: A Structural Characterization. Authors: Ruszkowski, M. / Sekula, B. / Ruszkowska, A. / Dauter, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ccz.cif.gz | 348.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ccz.ent.gz | 291.1 KB | Display | PDB format |
PDBx/mmJSON format | 6ccz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cc/6ccz ftp://data.pdbj.org/pub/pdb/validation_reports/cc/6ccz | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 49816.586 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: 11445860, MTR_2g018290 / Plasmid: pMCSG68 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: G7ILW0, glycine hydroxymethyltransferase |
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#2: Protein | Mass: 49588.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: 11445860, MTR_2g018290 / Plasmid: pMCSG68 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: G7ILW0, glycine hydroxymethyltransferase |
-Non-polymers , 4 types, 349 molecules
#3: Chemical | ChemComp-SEY / #4: Chemical | #5: Chemical | #6: 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: 2.48 Å3/Da / Density % sol: 50.33 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 55% Tacsimate pH 7.0; for SAD phasing crystals were transferred into a drop of 100% Tacsimate pH 7.0 with a single crystal of selenourea and soaked for 15 min |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9778 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Dec 7, 2017 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→100 Å / Num. obs: 52956 / % possible obs: 96.9 % / Redundancy: 6 % / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.085 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 2.14→2.27 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 7076 / Rrim(I) all: 0.88 / % possible all: 81.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.14→83.53 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.927 / SU B: 9.882 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.168 / 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: 35.656 Å2
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Refinement step | Cycle: 1 / Resolution: 2.14→83.53 Å
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Refine LS restraints |
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