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- PDB-1cj0: CRYSTAL STRUCTURE OF RABBIT CYTOSOLIC SERINE HYDROXYMETHYLTRANSFE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1cj0 | ||||||
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Title | CRYSTAL STRUCTURE OF RABBIT CYTOSOLIC SERINE HYDROXYMETHYLTRANSFERASE AT 2.8 ANGSTROM RESOLUTION | ||||||
![]() | PROTEIN (SERINE HYDROXYMETHYLTRANSFERASE) | ||||||
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Function / homology | ![]() cellular response to tetrahydrofolate / purine nucleobase biosynthetic process / L-serine metabolic process / glycine metabolic process / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Scarsdale, J.N. / Kazanina, G. / Radaev, S. / Schirch, V. / Wright, H.T. | ||||||
![]() | ![]() Title: Crystal structure of rabbit cytosolic serine hydroxymethyltransferase at 2.8 A resolution: mechanistic implications. Authors: Scarsdale, J.N. / Kazanina, G. / Radaev, S. / 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 | ![]() | 169.3 KB | Display | ![]() |
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PDB format | ![]() | 135.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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 oper: (Code: given Matrix: (-0.172468, -0.82198, 0.542773), Vector ![]() |
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Components
#1: Protein | Mass: 51706.785 Da / Num. of mol.: 2 / Mutation: N5Q Source method: isolated from a genetically manipulated source Details: EACH PROTEIN MOLECULE HAS COVALENTLY LINKED PLP COFACTOR Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ![]() #3: Water | ChemComp-HOH / | ![]() Sequence details | NO ELECTRON DENSITY WAS OBSERVED FOR THE FIRST 13 RESIDUES. IN CASES WHERE NO SIDECHAIN ELECTRON ...NO ELECTRON DENSITY WAS OBSERVED FOR THE FIRST 13 RESIDUES. IN CASES WHERE NO SIDECHAIN ELECTRON DENSITY WAS OBSERVED, RESIDUES WERE MODELED AS ALA DURING THE REFINEMENT | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 57 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | Method: vapor diffusion, hanging drop / pH: 6 Details: 20MM K2HPO4, KH2PO4, 25MM POTASIUM MES OR SODIUM HEPES, PH 7.0 0.2 MM 2-MERCAPTOETHANOL, 3% PEG 400, pH 6.0, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.8→35 Å / Num. obs: 28327 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 19 % / Biso Wilson estimate: 88.8 Å2 / Rmerge(I) obs: 0.173 / Net I/σ(I): 10.9 |
Reflection shell | *PLUS Mean I/σ(I) obs: 1 |
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Processing
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Refinement | Method to determine structure![]() ![]() Details: PROTEIN+PLP REFINED WITH TORSION ANGLE DYNAMICS, WATERS HELD FIXED. WATERS REFINED WITH CARTESIAN DYNAMICS, PROTEIN + PLP HELD FIXED. POSITIONAL NCS RESTRAINTS APPLIED BETWEEN EQUIVALENT ...Details: PROTEIN+PLP REFINED WITH TORSION ANGLE DYNAMICS, WATERS HELD FIXED. WATERS REFINED WITH CARTESIAN DYNAMICS, PROTEIN + PLP HELD FIXED. POSITIONAL NCS RESTRAINTS APPLIED BETWEEN EQUIVALENT RESIDUES IN CHAINS A + B. RESIDUES 9992- 1, 244-247, 4181-4180 AND 2291 WERE NOT RESTRAINED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 28.08 Å2 / ksol: 0.236 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINED / Rms dev position: 0.108 Å / Weight position: 150 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.97 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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