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Yorodumi- PDB-6czy: Crystal structure of Arabidopsis thaliana phosphoserine aminotran... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6czy | ||||||
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Title | Crystal structure of Arabidopsis thaliana phosphoserine aminotransferase isoform 1 (AtPSAT1) in complex with Pyridoxamine-5'-phosphate (PMP) | ||||||
Components | Phosphoserine aminotransferase 1, chloroplastic | ||||||
Keywords | TRANSFERASE / serine biosynthesis / pyridoxal 5'-phosphate / PLP / transaminase / PSAT / pyridoxamine / PMP | ||||||
Function / homology | Function and homology information phosphoserine transaminase / O-phospho-L-serine:2-oxoglutarate aminotransferase activity / L-serine biosynthetic process / plastid / chloroplast stroma / chloroplast / pyridoxal phosphate binding / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Sekula, B. / Ruszkowski, M. / Dauter, Z. | ||||||
Funding support | United States, 1items
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Citation | Journal: Front Plant Sci / Year: 2018 Title: Structural Analysis of Phosphoserine Aminotransferase (Isoform 1) FromArabidopsis thaliana- the Enzyme Involved in the Phosphorylated Pathway of Serine Biosynthesis. Authors: Sekula, B. / Ruszkowski, M. / Dauter, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6czy.cif.gz | 595.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6czy.ent.gz | 491.6 KB | Display | PDB format |
PDBx/mmJSON format | 6czy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6czy_validation.pdf.gz | 491 KB | Display | wwPDB validaton report |
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Full document | 6czy_full_validation.pdf.gz | 497.3 KB | Display | |
Data in XML | 6czy_validation.xml.gz | 72.2 KB | Display | |
Data in CIF | 6czy_validation.cif.gz | 111.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/6czy ftp://data.pdbj.org/pub/pdb/validation_reports/cz/6czy | HTTPS FTP |
-Related structure data
Related structure data | 6czxC 6czzC 4xk1S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 40276.176 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Tissue: Leaves / Gene: PSAT1, At4g35630, F8D20.140 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96255, phosphoserine transaminase |
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-Non-polymers , 6 types, 2046 molecules
#2: Chemical | ChemComp-PMP / #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | ChemComp-NA / | #6: Chemical | ChemComp-MPD / ( | #7: 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: 2.63 Å3/Da / Density % sol: 53.16 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M lithium sulfate, 17% PEG 3350 and 0.1 M Tris at pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2018 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→77.14 Å / Num. obs: 170626 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.75→1.85 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.915 / Mean I/σ(I) obs: 2.14 / Num. unique obs: 26555 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XK1 Resolution: 1.75→77.14 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.179 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.093 / 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: 22.936 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→77.14 Å
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Refine LS restraints |
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