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- PDB-6uxj: Structure of serine hydroxymethyltransferase 8 from Glycine max c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6uxj | ||||||
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Title | Structure of serine hydroxymethyltransferase 8 from Glycine max cultivar Essex complexed with PLP-glycine and 5-formyltetrahydrofolate | ||||||
![]() | Serine hydroxymethyltransferase | ||||||
![]() | PLANT PROTEIN / TRANSFERASE / folate metabolism / methyltransferase / soybean cyst nematode infection resistance / cytoplasmic enzyme | ||||||
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 / chloroplast / methyltransferase activity / cellular response to leukemia inhibitory factor / mRNA 5'-UTR binding / pyridoxal phosphate binding / methylation / protein homotetramerization / protein homodimerization activity / zinc ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Korasick, D.A. / Tanner, J.J. / Beamer, L.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Impaired folate binding of serine hydroxymethyltransferase 8 from soybean underlies resistance to the soybean cyst nematode. Authors: Korasick, D.A. / 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 | ![]() | 772.1 KB | Display | ![]() |
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PDB format | ![]() | 638.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 882.5 KB | Display | ![]() |
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Full document | ![]() | 903.1 KB | Display | |
Data in XML | ![]() | 3.7 KB | Display | |
Data in CIF | ![]() | 29.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6uxhSC ![]() 6uxiC ![]() 6uxkC ![]() 6uxlC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 52057.082 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: K4FZF8, UniProt: A0A0R0IK90*PLUS, glycine hydroxymethyltransferase #2: Chemical | ChemComp-PLG / #3: Chemical | ChemComp-FFO / #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.24 M trimethylamine N-oxide, 0.1 M Tris (pH 8.5), 20% (w/v) PEG MME 2000, 10 mM 5-formyl tetrahydrofolate, 20 mM glycine |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Apr 29, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→47.95 Å / Num. obs: 440251 / % possible obs: 98.5 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.044 / Rrim(I) all: 0.083 / Net I/σ(I): 10.2 / Num. measured all: 1533812 / Scaling rejects: 1836 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.019 / Num. measured all: 68936 / Num. unique obs: 21837 / CC1/2: 0.504 / Rpim(I) all: 0.67 / Rrim(I) all: 1.225 / Net I/σ(I) obs: 1 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6UXH Resolution: 1.4→45.382 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 18.59
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.95 Å2 / Biso mean: 19.205 Å2 / Biso min: 7.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4→45.382 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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