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- PDB-1ls3: Crystal Structure of the Complex between Rabbit Cytosolic Serine ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ls3 | ||||||
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Title | Crystal Structure of the Complex between Rabbit Cytosolic Serine Hydroxymethyltransferase and TriGlu-5-formyl-tetrahydrofolate | ||||||
![]() | Serine Hydroxymethyltransferase | ||||||
![]() | TRANSFERASE / asymmetric tetramer | ||||||
Function / homology | ![]() cellular response to tetrahydrofolate / purine nucleobase biosynthetic process / L-serine metabolic process / glycine metabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / L-serine catabolic process / tetrahydrofolate metabolic process ...cellular response to tetrahydrofolate / purine nucleobase biosynthetic process / L-serine metabolic process / glycine metabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / L-serine catabolic process / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / cobalt ion 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 / protein homotetramerization / protein homodimerization activity / zinc ion binding / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Fu, T.F. / Scarsdale, J.N. / Kazanina, G. / Schirch, V. / Wright, H.T. | ||||||
![]() | ![]() Title: Location of the Pteroylpolyglutamate Binding Site on Rabbit Cytosolic Serine Hydroxymethyltransferase Authors: Fu, T.F. / Scarsdale, J.N. / Kazanina, G. / Schirch, V. / Wright, H.T. | ||||||
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 | ![]() | 275.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 76.8 KB | Display | |
Data in CIF | ![]() | 102.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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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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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 52916.113 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: p07511, UniProt: P07511*PLUS, glycine hydroxymethyltransferase |
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-Non-polymers , 5 types, 390 molecules ![](data/chem/img/PLP.gif)
![](data/chem/img/GLY.gif)
![](data/chem/img/TGF.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GLY.gif)
![](data/chem/img/TGF.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PLP / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 50.9 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: small tubes / pH: 7 Details: 50 mg/ml Shmt 3% PEG 4000 50 mM Potassium-2(N-morpholino-)ethanesulfonate, pH 7.0, SMALL TUBES, temperature 298K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown / Details: used seeding | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Dec 7, 2000 / Details: Osmic Confocal optics |
Radiation | Monochromator: Osmic Confocal Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→99 Å / Num. all: 55833 / Num. obs: 48527 / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Biso Wilson estimate: 46.1 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 1.67 / % possible all: 93.6 |
Reflection | *PLUS Num. obs: 48537 / % possible obs: 87 % / Rmerge(I) obs: 0.08 |
Reflection shell | *PLUS % possible obs: 94 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2.1 Angstrom Structure of Rabbit Cytosolic Serine Hydroxymethyltransferase Resolution: 2.7→19.79 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 960476 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.9412 Å2 / ksol: 0.267359 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→19.79 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 20 Å / Rfactor Rwork: 0.22 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.406 / Rfactor Rwork: 0.321 |