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Yorodumi- PDB-5zfk: UDP Glucose alpha tetrahydrobiopterin glycosyltransferase from Sy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zfk | ||||||
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Title | UDP Glucose alpha tetrahydrobiopterin glycosyltransferase from Synechococcus species PCC 7942 - UDP-BH2 complex | ||||||
Components | (UDP-glucose:tetrahydrobiopterin glucosyltransferase) x 2 | ||||||
Keywords | TRANSFERASE / Tetrahydrobiopterin / UDPglucose / Pteridine glycosyltransferase / Pteridine glycosides / Synechococcus. | ||||||
Function / homology | Glycosyl transferase, family 1 / Glycosyl transferases group 1 / glycosyltransferase activity / 7,8-DIHYDROBIOPTERIN / URIDINE-5'-DIPHOSPHATE / UDP-glucose:tetrahydrobiopterin glucosyltransferase / UDP-glucose:tetrahydrobiopterin glucosyltransferase Function and homology information | ||||||
Biological species | Synechococcus elongatus PCC 7942 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 | 5zfk.cif.gz | 160.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zfk.ent.gz | 123.3 KB | Display | PDB format |
PDBx/mmJSON format | 5zfk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zf/5zfk ftp://data.pdbj.org/pub/pdb/validation_reports/zf/5zfk | HTTPS FTP |
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-Related structure data
Related structure data | 5ze7SC 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 38406.992 Da / Num. of mol.: 1 / Fragment: UNP residues 2-355 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus elongatus PCC 7942 (bacteria) Strain: PCC 7942 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q93EY3, UniProt: Q31LX1*PLUS | ||
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#2: Protein | Mass: 38249.797 Da / Num. of mol.: 1 / Fragment: UNP residues 2-354 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus elongatus PCC 7942 (bacteria) Strain: PCC 7942 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q93EY3, UniProt: Q31LX1*PLUS | ||
#3: Chemical | ChemComp-UDP / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.96 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: Bis-tris, PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.979,0.979,0.987 | |||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2013 | |||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.75→50 Å / Num. obs: 71852 / % possible obs: 99.2 % / Redundancy: 3.7 % / Net I/σ(I): 14.5 | |||||||||
Reflection shell | Resolution: 1.75→1.78 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ZE7 Resolution: 1.75→50 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.435 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.104 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.19 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→50 Å
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Refine LS restraints |
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