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- PDB-1rv3: E75L MUTANT OF RABBIT CYTOSOLIC SERINE HYDROXYMETHYLTRANSFERASE, ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1rv3 | ||||||
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Title | E75L MUTANT OF RABBIT CYTOSOLIC SERINE HYDROXYMETHYLTRANSFERASE, COMPLEX WITH GLYCINE | ||||||
![]() | Serine hydroxymethyltransferase, cytosolic![]() | ||||||
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Function / homology | ![]() cellular response to tetrahydrofolate / purine nucleobase biosynthetic process / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Szebenyi, D.M. / Musayev, F.N. / di Salvo, M.L. / Safo, M.K. / Schirch, V. | ||||||
![]() | ![]() Title: Serine Hydroxymethyltransferase: Role of Glu75 and Evidence that Serine Is Cleaved by a Retroaldol Mechanism. Authors: Szebenyi, D.M. / Musayev, F.N. / di Salvo, M.L. / Safo, M.K. / Schirch, V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 189.5 KB | Display | ![]() |
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PDB format | ![]() | 150.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1rv4C ![]() 1rvuC ![]() 1rvyC ![]() 1cj0S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | The asymmetric unit contains a homodimer. The biological assembly is a tetramer consisting of a pair of dimers. The second dimer is generated by the operation: y,x,1-z. |
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Components
#1: Protein | ![]() Mass: 52900.156 Da / Num. of mol.: 2 / Mutation: E75L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: P07511, ![]() #2: Chemical | ![]() #3: Chemical | ![]() #4: Chemical | ChemComp-GLY / | ![]() #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 51.91 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: PEG 8000, KCl, potassium phosphate, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 6, 2003 / Details: White beam mirror, focussing monochromatic mirror |
Radiation | Monochromator: SI 111, bent triangle / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.4→48.9 Å / Num. all: 42150 / Num. obs: 42006 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13 % / Biso Wilson estimate: 51.8 Å2 / Rsym value: 0.1 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 12.2 % / Mean I/σ(I) obs: 1.3 / Num. unique all: 5998 / Rsym value: 0.566 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1CJ0 Resolution: 2.4→48.88 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2595470.56 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.7549 Å2 / ksol: 0.313623 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→48.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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