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Open data
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Basic information
Entry | Database: PDB / ID: 1eji | ||||||
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Title | RECOMBINANT SERINE HYDROXYMETHYLTRANSFERASE (MOUSE) | ||||||
![]() | SERINE HYDROXYMETHYLTRANSFERASE | ||||||
![]() | TRANSFERASE / SERINE-GLYCINE CONVERSION / PYRIDOXAL 5'-PHOSPHATE / TETRAHYDROFOLATE / ASYMMETRIC DIMER | ||||||
Function / homology | ![]() Carnitine synthesis / Metabolism of folate and pterines / cellular response to tetrahydrofolate / L-allo-threonine aldolase activity / glycine biosynthetic process / purine nucleobase biosynthetic process / L-serine metabolic process / glycine metabolic process / serine binding / L-serine catabolic process ...Carnitine synthesis / Metabolism of folate and pterines / cellular response to tetrahydrofolate / L-allo-threonine aldolase activity / glycine biosynthetic process / purine nucleobase biosynthetic process / L-serine metabolic process / glycine metabolic process / serine binding / L-serine catabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / dTMP biosynthetic process / amino acid binding / cobalt ion binding / small molecule binding / folic acid metabolic process / mRNA regulatory element binding translation repressor activity / cellular response to leukemia inhibitory factor / mRNA 5'-UTR binding / pyridoxal phosphate binding / one-carbon metabolic process / protein homotetramerization / negative regulation of translation / protein homodimerization activity / mitochondrion / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Szebenyi, D.M.E. / Liu, X. / Kriksunov, I.A. / Stover, P.J. / Thiel, D.J. | ||||||
![]() | ![]() Title: Structure of a murine cytoplasmic serine hydroxymethyltransferase quinonoid ternary complex: evidence for asymmetric obligate dimers. Authors: Szebenyi, D.M. / Liu, X. / Kriksunov, I.A. / Stover, P.J. / Thiel, D.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 337.1 KB | Display | ![]() |
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PDB format | ![]() | 291.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1cj0S 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:
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Components
#1: Protein | Mass: 53167.594 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P50431, glycine hydroxymethyltransferase #2: Chemical | ChemComp-PLG / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 62.3 % Description: RESOLUTION RANGES 3.96-3.84 AND 3.72-3.64 A EXCLUDED FROM PROCESSING BECAUSE OF ICE RINGS. | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.7 Details: 8% PEG 8000, 6% ETHYLENE GLYCOL, 0.1 M HEPES, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 7, 1999 / Details: MIRROR |
Radiation | Monochromator: BENT TRIANGULAR SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.922 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→32.1 Å / Num. obs: 57974 / % possible obs: 92.8 % / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Biso Wilson estimate: 78.8 Å2 / Rsym value: 0.203 / Net I/σ(I): 3.4 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 10.9 % / Mean I/σ(I) obs: 0.3 / Rsym value: 2.38 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 1046890 / Rmerge(I) obs: 0.203 |
Reflection shell | *PLUS % possible obs: 100 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: RABBIT SHMT (1CJ0) DIMER, WITH 2 PLP COFACTORS. EACH MONOMER WAS MODIFIED BY: OMISSION OF RESIDUES 269-287 (IN THE HUMAN SHMT NUMBERING SCHEME; LABELED 241-250 IN THE 1CJ0 ENTRY), ...Starting model: RABBIT SHMT (1CJ0) DIMER, WITH 2 PLP COFACTORS. EACH MONOMER WAS MODIFIED BY: OMISSION OF RESIDUES 269-287 (IN THE HUMAN SHMT NUMBERING SCHEME; LABELED 241-250 IN THE 1CJ0 ENTRY), CONVERSION OF ALL MET RESIDUES TO SEMET, AND CONVERSION TO ALANINE OF RESIDUES WHICH DIFFER BETWEEN RABBIT AND MOUSE, I.E. RESIDUES 16, 20, 35, 68, 88, 94, 175, 177, 182, 185, 191, 220, 237, 322, 326, 329, 332, 343, 361, 416, 433, 437-439, 441-442, 458, 460, 463, 467, 471, 475, AND 477 IN THE HUMAN SHMT NUMBERING SCHEME. Resolution: 2.9→32.1 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 66.13 Å2 / ksol: 0.347 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 84.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→32.1 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10.1 % / Rfactor Rfree: 0.272 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 84.6 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.379 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.371 |