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- PDB-6fl5: Structure of human SHMT1-H135N-R137A-E168N mutant at 3.6 Ang. res... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6fl5 | |||||||||||||||
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Title | Structure of human SHMT1-H135N-R137A-E168N mutant at 3.6 Ang. resolution | |||||||||||||||
![]() | Serine hydroxymethyltransferase, cytosolic | |||||||||||||||
![]() | TRANSFERASE / serine hydroxymethyltransferase / Interface / Tetramer / OCM / serine / THF / glicine / TCA | |||||||||||||||
Function / homology | ![]() cellular response to tetrahydrofolate / Carnitine synthesis / purine nucleobase biosynthetic process / L-serine metabolic process / glycine metabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / Metabolism of folate and pterines ...cellular response to tetrahydrofolate / Carnitine synthesis / purine nucleobase biosynthetic process / L-serine metabolic process / glycine metabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / Metabolism of folate and pterines / L-serine catabolic process / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / dTMP biosynthetic process / cobalt ion binding / folic acid metabolic process / small molecule binding / mRNA regulatory element binding translation repressor activity / cellular response to leukemia inhibitory factor / mRNA 5'-UTR binding / pyridoxal phosphate binding / protein homotetramerization / negative regulation of translation / protein homodimerization activity / mitochondrion / zinc ion binding / extracellular exosome / nucleoplasm / identical protein binding / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||||||||
![]() | Giardina, G. / Cutruzzola, F. / Lucchi, R. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: The catalytic activity of serine hydroxymethyltransferase is essential for de novo nuclear dTMP synthesis in lung cancer cells. Authors: Giardina, G. / Paone, A. / Tramonti, A. / Lucchi, R. / Marani, M. / Magnifico, M.C. / Bouzidi, A. / Pontecorvi, V. / Guiducci, G. / Zamparelli, C. / Rinaldo, S. / Paiardini, A. / ...Authors: Giardina, G. / Paone, A. / Tramonti, A. / Lucchi, R. / Marani, M. / Magnifico, M.C. / Bouzidi, A. / Pontecorvi, V. / Guiducci, G. / Zamparelli, C. / Rinaldo, S. / Paiardini, A. / Contestabile, R. / Cutruzzola, F. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 358.7 KB | Display | ![]() |
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PDB format | ![]() | 292.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 340.6 KB | Display | ![]() |
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Full document | ![]() | 369.1 KB | Display | |
Data in XML | ![]() | 66.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1bj4S S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 1
NCS ensembles :
NCS oper:
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Components
#1: Protein | Mass: 51695.797 Da / Num. of mol.: 4 / Mutation: H135N, R137A, E168N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P34896, glycine hydroxymethyltransferase #2: Chemical | ChemComp-PLP / #3: Chemical | ChemComp-CL / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.24 % / Description: rod like crystals |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2 microL of 80microM protein solution in: 20 mM Hepes pH7.2, 250 mM NaCl 5% glycerol + 2 microL of reservoir:0.1 M Na Cacodilate pH6.5 - 1M Na citrate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Mar 10, 2017 / Details: CRL | ||||||||||||||||||||||||
Radiation | Monochromator: C(110) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 3.6→56.61 Å / Num. obs: 30938 / % possible obs: 98.2 % / Redundancy: 6.3 % / CC1/2: 0.973 / Rmerge(I) obs: 0.312 / Rpim(I) all: 0.131 / Rrim(I) all: 0.34 / Net I/σ(I): 5.6 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | ||||||
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Phasing MR | R rigid body: 0.57
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1BJ4 Resolution: 3.6→50.01 Å / Cor.coef. Fo:Fc: 0.865 / Cor.coef. Fo:Fc free: 0.83 / SU B: 44.648 / SU ML: 0.62 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.716 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 160.73 Å2 / Biso mean: 74.364 Å2 / Biso min: 19.04 Å2
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Refinement step | Cycle: final / Resolution: 3.6→50.01 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.87
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LS refinement shell | Resolution: 3.6→3.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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