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- PDB-4wxb: Crystal Structure of Serine Hydroxymethyltransferase from Strepto... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4wxb | ||||||||||||
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Title | Crystal Structure of Serine Hydroxymethyltransferase from Streptococcus thermophilus | ||||||||||||
![]() | Serine hydroxymethyltransferase | ||||||||||||
![]() | TRANSFERASE / Aldolase / Serine hydrodymethyltransferase / Aldehydes / Catalysis / Catalytic Domain / Escherichia coli / Chemical / Protein Binding / Protein Conformation / Protein Structure | ||||||||||||
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 | ![]() ![]() ![]() | ||||||||||||
![]() | Hernandez, K. / Zelen, I. / Petrillo, G. / Uson, I. / Wandtke, C. / Bujons, J. / Joglar, J. / Parella, T. / Clapes, P. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Engineered L-Serine Hydroxymethyltransferase from Streptococcus thermophilus for the Synthesis of alpha , alpha-Dialkyl-alpha-Amino Acids. Authors: Hernandez, K. / Zelen, I. / Petrillo, G. / Uson, I. / Wandtke, C.M. / Bujons, J. / Joglar, J. / Parella, T. / Clapes, P. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 329.1 KB | Display | ![]() |
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PDB format | ![]() | 265.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4wxfC ![]() 4wxgC ![]() 1kkjS 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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 46543.543 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q5M0B4, glycine hydroxymethyltransferase |
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-Non-polymers , 5 types, 593 molecules ![](data/chem/img/CIT.gif)
![](data/chem/img/CAC.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CAC.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CIT / #3: Chemical | ChemComp-CAC / #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.1 Å3/Da / Density % sol: 69.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: HEPES 20 mM, pH 7,5 Sodium citrate 0.8-1.2 M Cacodylate 1 M, pH 6,5 |
-Data collection
Diffraction | Mean temperature: 100 K Ambient temp details: data merged from two crystals collected on the same day Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 29, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→78.1 Å / Num. obs: 187621 / % possible obs: 98.8 % / Redundancy: 8 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.05→2.15 Å / Redundancy: 1.96 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 2 / Num. unique obs: 15884 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1KKJ Resolution: 2.05→66.54 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.151 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 120.74 Å2 / Biso mean: 38.37 Å2 / Biso min: 17.52 Å2
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Refinement step | Cycle: final / Resolution: 2.05→66.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.1 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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