+Open data
-Basic information
Entry | Database: PDB / ID: 1eji | ||||||
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Title | RECOMBINANT SERINE HYDROXYMETHYLTRANSFERASE (MOUSE) | ||||||
Components | SERINE HYDROXYMETHYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / SERINE-GLYCINE CONVERSION / PYRIDOXAL 5'-PHOSPHATE / TETRAHYDROFOLATE / ASYMMETRIC DIMER | ||||||
Function / homology | Function and homology information Carnitine synthesis / Metabolism of folate and pterines / cellular response to tetrahydrofolate / L-allo-threonine aldolase activity / purine nucleobase biosynthetic process / serine binding / L-serine catabolic process / L-serine metabolic process / glycine metabolic process / glycine hydroxymethyltransferase ...Carnitine synthesis / Metabolism of folate and pterines / cellular response to tetrahydrofolate / L-allo-threonine aldolase activity / purine nucleobase biosynthetic process / serine binding / L-serine catabolic process / L-serine metabolic process / glycine metabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate metabolic process / cobalt ion binding / tetrahydrofolate interconversion / dTMP biosynthetic process / amino acid binding / folic acid metabolic process / small molecule binding / glycine biosynthetic process / cellular response to leukemia inhibitory factor / mRNA regulatory element binding translation repressor activity / 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 | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Szebenyi, D.M.E. / Liu, X. / Kriksunov, I.A. / Stover, P.J. / Thiel, D.J. | ||||||
Citation | Journal: Biochemistry / Year: 2000 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1eji.cif.gz | 337.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eji.ent.gz | 291.9 KB | Display | PDB format |
PDBx/mmJSON format | 1eji.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/1eji ftp://data.pdbj.org/pub/pdb/validation_reports/ej/1eji | 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 |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Mus musculus (house mouse) / Organ: LIVER / Plasmid: PET28A(+) / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) References: UniProt: P50431, glycine hydroxymethyltransferase #2: Chemical | ChemComp-PLG / #3: Chemical | #4: 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: 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: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.922 |
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 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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 |