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- PDB-4p3m: Crystal structure of serine hydroxymethyltransferase from Psychro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4p3m | ||||||
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Title | Crystal structure of serine hydroxymethyltransferase from Psychromonas ingrahamii | ||||||
![]() | Serine hydroxymethyltransferase | ||||||
![]() | TRANSFERASE / SERINE HYDROXYMETHYLTRANSFERASE / PYRIDOXAL PHOSPHATE / PSYCHROPHILIC ENZYME | ||||||
Function / homology | ![]() glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / pyridoxal phosphate binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dworkowski, F. / Angelaccio, S. / Pascarella, S. / Capitani, G. | ||||||
![]() | ![]() Title: Conformational transitions driven by pyridoxal-5'-phosphate uptake in the psychrophilic serine hydroxymethyltransferase from Psychromonas ingrahamii. Authors: Angelaccio, S. / Dworkowski, F. / Di Bello, A. / Milano, T. / Capitani, G. / Pascarella, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 296.2 KB | Display | ![]() |
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PDB format | ![]() | 243.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 471.9 KB | Display | ![]() |
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Full document | ![]() | 480.2 KB | Display | |
Data in XML | ![]() | 34.3 KB | Display | |
Data in CIF | ![]() | 51.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3gbxS 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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Components
#1: Protein | Mass: 46302.383 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A1SUU0, glycine hydroxymethyltransferase #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.75 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 2 M AMMONIUM SULFATE, 150 mM SODIUM CHLORIDE, 100 mM SODIUM CACODYLATE pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 5, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→47.61 Å / Num. obs: 76583 / % possible obs: 99.7 % / Redundancy: 6.8 % / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.85→1.9 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 0.96 / % possible all: 99.8 |
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Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3gbx Resolution: 1.85→47.609 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 20.81 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→47.609 Å
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Refine LS restraints |
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LS refinement shell |
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