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Yorodumi- PDB-4wxb: Crystal Structure of Serine Hydroxymethyltransferase from Strepto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wxb | ||||||||||||
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Title | Crystal Structure of Serine Hydroxymethyltransferase from Streptococcus thermophilus | ||||||||||||
Components | Serine hydroxymethyltransferase | ||||||||||||
Keywords | TRANSFERASE / Aldolase / Serine hydrodymethyltransferase / Aldehydes / Catalysis / Catalytic Domain / Escherichia coli / Chemical / Protein Binding / Protein Conformation / Protein Structure | ||||||||||||
Function / homology | Function and homology information glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / L-serine catabolic process / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / pyridoxal phosphate binding / zinc ion binding / cytosol Similarity search - Function | ||||||||||||
Biological species | Streptococcus thermophilus (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||||||||
Authors | Hernandez, K. / Zelen, I. / Petrillo, G. / Uson, I. / Wandtke, C. / Bujons, J. / Joglar, J. / Parella, T. / Clapes, P. | ||||||||||||
Funding support | Spain, 2items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wxb.cif.gz | 329.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wxb.ent.gz | 265.9 KB | Display | PDB format |
PDBx/mmJSON format | 4wxb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wxb_validation.pdf.gz | 5.5 MB | Display | wwPDB validaton report |
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Full document | 4wxb_full_validation.pdf.gz | 5.5 MB | Display | |
Data in XML | 4wxb_validation.xml.gz | 64.7 KB | Display | |
Data in CIF | 4wxb_validation.cif.gz | 89.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wx/4wxb ftp://data.pdbj.org/pub/pdb/validation_reports/wx/4wxb | HTTPS FTP |
-Related structure data
Related structure data | 4wxfC 4wxgC 1kkjS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Streptococcus thermophilus (bacteria) / Strain: CNRZ 1066 / Gene: glyA, str0755 / Production host: Escherichia coli (E. coli) References: UniProt: Q5M0B4, glycine hydroxymethyltransferase |
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-Non-polymers , 5 types, 593 molecules
#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: X-RAY DIFFRACTION |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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