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- PDB-8dom: Structure of the N358Y single variant ofserine hydroxymethyltrans... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8dom | ||||||
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Title | Structure of the N358Y single variant ofserine hydroxymethyltransferase 8 from Glycine max cultivar Essex complexed with PLP | ||||||
![]() | Serine hydroxymethyltransferase | ||||||
![]() | TRANSFERASE / Enzyme / complex | ||||||
Function / homology | ![]() purine nucleobase biosynthetic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / L-serine catabolic process / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / mRNA regulatory element binding translation repressor activity ...purine nucleobase biosynthetic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / L-serine catabolic process / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / mRNA regulatory element binding translation repressor activity / cellular response to leukemia inhibitory factor / mRNA 5'-UTR binding / pyridoxal phosphate binding / protein homotetramerization / protein homodimerization activity / zinc ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Korasick, D.A. / Beamer, L.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and functional analysis of two SHMT8 variants associated with soybean cyst nematode resistance. Authors: Korasick, D.A. / Owuocha, L.F. / Kandoth, P.K. / Tanner, J.J. / Mitchum, M.G. / Beamer, L.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 453.7 KB | Display | ![]() |
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PDB format | ![]() | 306.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.2 KB | Display | ![]() |
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Full document | ![]() | 459.9 KB | Display | |
Data in XML | ![]() | 37 KB | Display | |
Data in CIF | ![]() | 53.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ujhC ![]() 7ujiC ![]() 8dskC ![]() 8fsdC ![]() 6uxhS C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 54418.543 Da / Num. of mol.: 2 / Mutation: N358Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A0A0R0IK90, glycine hydroxymethyltransferase #2: Chemical | ChemComp-EDO / | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.18 - 0.25 TMAO 0.1 M Tris (ph 8.5) 21-23 (w/v) % PEG MME 2000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→128.63 Å / Num. obs: 75185 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 44.98 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.027 / Rrim(I) all: 0.075 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.89→1.93 Å / Redundancy: 7.6 % / Rmerge(I) obs: 4.323 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 33413 / CC1/2: 0.339 / Rpim(I) all: 1.678 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6uxh Resolution: 1.89→64.31 Å / SU ML: 0.2962 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 25.8322 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.89→64.31 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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