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Yorodumi- PDB-5ze7: UDP Glucose alpha tetrahydrobiopterin glycosyltransferase from Sy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ze7 | ||||||
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Title | UDP Glucose alpha tetrahydrobiopterin glycosyltransferase from Synechococcus species PCC 7942 - apo form | ||||||
Components | UDP-glucose:tetrahydrobiopterin glucosyltransferase | ||||||
Keywords | TRANSFERASE / Tetrahydrobiopterin / UDPglucose / Pteridine glycosyltransferase / Pteridine glycosides / Synechococcus. | ||||||
Function / homology | : / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / glycosyltransferase activity / nucleotide binding / UDP-glucose:tetrahydrobiopterin glucosyltransferase / UDP-glucose:tetrahydrobiopterin glucosyltransferase Function and homology information | ||||||
Biological species | Synechococcus elongatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.99 Å | ||||||
Authors | Killivalavan, A. / Lee, K.H. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: To Be Published Title: UDP Glucose alpha tetrahydrobiopterin glycosyltransferase from Synechococcus species PCC 7942 - apo form Authors: Killivalavan, A. / Lee, K.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ze7.cif.gz | 267.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ze7.ent.gz | 224.5 KB | Display | PDB format |
PDBx/mmJSON format | 5ze7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ze7_validation.pdf.gz | 432.2 KB | Display | wwPDB validaton report |
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Full document | 5ze7_full_validation.pdf.gz | 441 KB | Display | |
Data in XML | 5ze7_validation.xml.gz | 27.6 KB | Display | |
Data in CIF | 5ze7_validation.cif.gz | 39.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/5ze7 ftp://data.pdbj.org/pub/pdb/validation_reports/ze/5ze7 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38249.797 Da / Num. of mol.: 2 / Fragment: UNP residues 2-354 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus elongatus (strain PCC 7942) (bacteria) Strain: PCC 7942 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q93EY3, UniProt: Q31LX1*PLUS #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.62 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: Bis-tris, PEG 3350, Galactose |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.979, 0.979,0.964 | ||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 28, 2013 | ||||||||||||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection |
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Reflection shell | Resolution: 1.99→2.02 Å |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.99→45.447 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.04 / 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: 1.99→45.447 Å
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Refine LS restraints |
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LS refinement shell |
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