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Yorodumi- PDB-6smn: A. thaliana serine hydroxymethyltransferase isoform 2 (AtSHMT2) i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6smn | ||||||
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Title | A. thaliana serine hydroxymethyltransferase isoform 2 (AtSHMT2) in complex with methotrexate | ||||||
Components | (Serine hydroxymethyltransferase 2, ...) x 2 | ||||||
Keywords | TRANSFERASE / SHMT / antifolate | ||||||
Function / homology | Function and homology information L-serine metabolic process / glycine metabolic process / serine binding / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / L-serine catabolic process / tetrahydrofolate interconversion / plastid / cobalt ion binding ...L-serine metabolic process / glycine metabolic process / serine binding / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / L-serine catabolic process / tetrahydrofolate interconversion / plastid / cobalt ion binding / mitochondrial respiratory chain complex I / folic acid metabolic process / pyridoxal phosphate binding / mitochondrion / zinc ion binding Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | ||||||
Authors | Ruszkowski, M. / Sekula, B. / Dauter, Z. | ||||||
Citation | Journal: Sci Rep / Year: 2019 Title: Structural basis of methotrexate and pemetrexed action on serine hydroxymethyltransferases revealed using plant models. Authors: Ruszkowski, M. / Sekula, B. / Ruszkowska, A. / Contestabile, R. / Nogues, I. / Angelaccio, S. / Szczepaniak, 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 | 6smn.cif.gz | 869.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6smn.ent.gz | 705.2 KB | Display | PDB format |
PDBx/mmJSON format | 6smn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sm/6smn ftp://data.pdbj.org/pub/pdb/validation_reports/sm/6smn | HTTPS FTP |
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-Related structure data
Related structure data | 6smrC 6smwC 6cd0S 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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Unit cell |
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-Components
-Serine hydroxymethyltransferase 2, ... , 2 types, 4 molecules ABCD
#1: Protein | Mass: 53545.035 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SHM2, SHMT2, At5g26780, F2P16.40 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Gold References: UniProt: Q94C74, glycine hydroxymethyltransferase #2: Protein | | Mass: 53773.156 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SHM2, SHMT2, At5g26780, F2P16.40 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Gold References: UniProt: Q94C74, glycine hydroxymethyltransferase |
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-Non-polymers , 5 types, 1978 molecules
#3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-MTX / #6: Chemical | ChemComp-SER / | #7: Water | ChemComp-HOH / | |
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-Details
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: 2.64 Å3/Da / Density % sol: 53.37 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 3 uL of the protein solution and 2 uL of reservoir solution: 90% Hampton Research Index F8 (0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5, and 25% polyethylene glycol 3350). Mature crystals ...Details: 3 uL of the protein solution and 2 uL of reservoir solution: 90% Hampton Research Index F8 (0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5, and 25% polyethylene glycol 3350). Mature crystals were transferred to drops with the original screen conditions supplemented with 20% ethylene glycol, 50 mM L-serine, and 10 mM MTX. After 24-h incubation, crystals were harvested and vitrified in liquid nitrogen. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Aug 10, 2018 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→80 Å / Num. obs: 279297 / % possible obs: 99.8 % / Redundancy: 8.2 % / CC1/2: 1 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.093 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 1.63→1.73 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1.16 / Mean I/σ(I) obs: 2 / Num. unique obs: 44247 / CC1/2: 0.7 / Rrim(I) all: 1.24 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6cd0 Resolution: 1.63→80 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 1.63→80 Å
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Refine LS restraints |
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