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Yorodumi- PDB-6m5o: Co-crystal structure of human serine hydroxymethyltransferase 2 i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6m5o | ||||||
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Title | Co-crystal structure of human serine hydroxymethyltransferase 2 in complex with Pyridoxal 5'-phosphate (PLP) and glycodeoxycholic acid | ||||||
Components | Serine hydroxymethyltransferase, mitochondrial | ||||||
Keywords | TRANSFERASE / Inhibitor / Complex | ||||||
Function / homology | Function and homology information BRISC complex / L-allo-threonine aldolase activity / regulation of mitochondrial translation / L-serine metabolic process / glycine metabolic process / L-serine biosynthetic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / Metabolism of folate and pterines ...BRISC complex / L-allo-threonine aldolase activity / regulation of mitochondrial translation / L-serine metabolic process / glycine metabolic process / L-serine biosynthetic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / Metabolism of folate and pterines / regulation of oxidative phosphorylation / tetrahydrofolate metabolic process / response to type I interferon / protein K63-linked deubiquitination / tetrahydrofolate interconversion / regulation of aerobic respiration / amino acid binding / mitochondrial nucleoid / RHOG GTPase cycle / Mitochondrial protein degradation / protein tetramerization / microtubule cytoskeleton / pyridoxal phosphate binding / one-carbon metabolic process / protein homotetramerization / mitochondrial inner membrane / mitochondrial matrix / positive regulation of cell population proliferation / chromatin binding / mitochondrion / extracellular exosome / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.30000663987 Å | ||||||
Authors | Ota, T. / Senoo, A. / Ito, S. / Ueno, G. / Nagatoishi, S. / Tsumoto, K. / Sando, S. | ||||||
Citation | Journal: Iscience / Year: 2021 Title: Structural basis for selective inhibition of human serine hydroxymethyltransferase by secondary bile acid conjugate. Authors: Ota, T. / Senoo, A. / Shirakawa, M. / Nonaka, H. / Saito, Y. / Ito, S. / Ueno, G. / Nagatoishi, S. / Tsumoto, K. / Sando, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6m5o.cif.gz | 463.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m5o.ent.gz | 313.9 KB | Display | PDB format |
PDBx/mmJSON format | 6m5o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6m5o_validation.pdf.gz | 1015.8 KB | Display | wwPDB validaton report |
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Full document | 6m5o_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6m5o_validation.xml.gz | 41.7 KB | Display | |
Data in CIF | 6m5o_validation.cif.gz | 59.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m5/6m5o ftp://data.pdbj.org/pub/pdb/validation_reports/m5/6m5o | HTTPS FTP |
-Related structure data
Related structure data | 6m5wC 4pvfS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 56342.805 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SHMT2 / Production host: Escherichia coli (E. coli) References: UniProt: P34897, glycine hydroxymethyltransferase #2: Chemical | #3: Chemical | #4: 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: 3.43 Å3/Da / Density % sol: 64.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris hydrochloride pH 8.5, 8% (w/v) polyethylene glycol 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: May 28, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→49.3564705048 Å / Num. obs: 70999 / % possible obs: 100 % / Redundancy: 22.25 % / Rmerge(I) obs: 0.316 / Rrim(I) all: 0.324 / Net I/σ(I): 12.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PVF Resolution: 2.30000663987→49.3564705048 Å / SU ML: 0.303512515499 / Cross valid method: FREE R-VALUE / σ(F): 1.35660850073 / Phase error: 26.6768656715
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.9272779355 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.30000663987→49.3564705048 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 |
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