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Yorodumi- PDB-7uji: Structure of the P130R single variant of serine hydroxymethyltran... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7uji | ||||||
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Title | Structure of the P130R single variant of serine hydroxymethyltransferase 8 from Glycine max cultivar Essex complexed with PLP | ||||||
Components | Serine hydroxymethyltransferase | ||||||
Keywords | TRANSFERASE / Enzyme / complex | ||||||
Function / homology | Function and homology information glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Glycine max (soybean) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å | ||||||
Authors | Korasick, D.A. / Beamer, L.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Febs J. / Year: 2024 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. #1: Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams / Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7uji.cif.gz | 443 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7uji.ent.gz | 299.8 KB | Display | PDB format |
PDBx/mmJSON format | 7uji.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7uji_validation.pdf.gz | 458.7 KB | Display | wwPDB validaton report |
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Full document | 7uji_full_validation.pdf.gz | 466.3 KB | Display | |
Data in XML | 7uji_validation.xml.gz | 35.8 KB | Display | |
Data in CIF | 7uji_validation.cif.gz | 50.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uj/7uji ftp://data.pdbj.org/pub/pdb/validation_reports/uj/7uji | HTTPS FTP |
-Related structure data
Related structure data | 7ujhC 8domC 8dskC 8fsdC 1uxhS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 54291.406 Da / Num. of mol.: 2 / Mutation: P130R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Glycine max (soybean) / Gene: 100305380, GLYMA_08G108900 / Variant: P130R / Production host: Escherichia coli (E. coli) References: UniProt: A0A0R0IK90, glycine hydroxymethyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.19 Å3/Da / Density % sol: 43.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.8 - 0.25 M trimethylamine N-oxide, 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: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.000003 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Oct 22, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.000003 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→47.47 Å / Num. obs: 41612 / % possible obs: 99.74 % / Redundancy: 7.1 % / Biso Wilson estimate: 42.14 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.05908 / Rrim(I) all: 0.1577 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 27361 / CC1/2: 0.469 / Rpim(I) all: 0.9639 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1uxh Resolution: 2.3→47.47 Å / SU ML: 0.317 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.3997 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: 46.64 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→47.47 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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