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- PDB-6yrw: SHMT from Streptococcus thermophilus Tyr55Ser variant as internal... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6yrw | ||||||
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Title | SHMT from Streptococcus thermophilus Tyr55Ser variant as internal aldimine and as non-covalent complex with D-Ser | ||||||
![]() | Serine hydroxymethyltransferase | ||||||
![]() | TRANSFERASE / Pyridoxal phosphate / X-ray crystallography / hydroxymethyltransferase / proton abstraction / tetrahydrofolate-independent | ||||||
Function / homology | ![]() serine binding / L-serine catabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / pyridoxal phosphate binding / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Petrillo, G. / Hernandez, K. / Bujons, J. / Clapes, P. / Uson, I. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into nucleophile substrate specificity in variants of N-Serine hydroxymethyltransferase from Streptococcus thermophilus Authors: Petrillo, G. / Hernandez, K. / Bujons, J. / Clapes, P. / Uson, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 321.9 KB | Display | ![]() |
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PDB format | ![]() | 263.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6tghC ![]() 6ti1C ![]() 6ti3C ![]() 4wxgS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 45061.926 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q5MCK9, UniProt: Q5M0B4*PLUS, glycine hydroxymethyltransferase #2: Chemical | ChemComp-PLP / #3: Chemical | ChemComp-DSN / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.24 Å3/Da / Density % sol: 70.97 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: PLP 5mM D-serine 100mM Cacodylate 0.1M ph 6.5 Sodium citrate 0.85M |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 16, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9697 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→47.85 Å / Num. obs: 80329 / % possible obs: 76.01 % / Redundancy: 1.59 % / CC1/2: 0.95 / Net I/σ(I): 41.89 |
Reflection shell | Resolution: 2.5→2.565 Å / Num. unique obs: 73924 / CC1/2: 0.95 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4WXG Resolution: 2.5→47.85 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / SU B: 8.8 / SU ML: 0.181 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.376 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 137.12 Å2 / Biso mean: 40.372 Å2 / Biso min: 3.2 Å2
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Refinement step | Cycle: final / Resolution: 2.5→47.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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