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Yorodumi- PDB-2p6p: X-ray crystal structure of C-C bond-forming dTDP-D-Olivose-transf... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2p6p | ||||||
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Title | X-ray crystal structure of C-C bond-forming dTDP-D-Olivose-transferase UrdGT2 | ||||||
Components | Glycosyl transferaseGlycosyltransferase | ||||||
Keywords | TRANSFERASE / C-glycosyltransferase / dTDP-D-Olivose-transferase / polyketide aglycon / GT-B family / X-ray-diffraction / UrdamycinA-biosynthesis | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces fradiae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.88 Å | ||||||
Authors | Mittler, M. / Bechthold, A. / Schulz, G.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Structure and action of the C-C bond-forming glycosyltransferase UrdGT2 involved in the biosynthesis of the antibiotic urdamycin. Authors: Mittler, M. / Bechthold, A. / Schulz, G.E. | ||||||
History |
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Remark 999 | SEQUENCE Author states that the sequence database reference that was used for this entry (UNP ...SEQUENCE Author states that the sequence database reference that was used for this entry (UNP Q9RPA7) does not match sequence. The DB ref was removed. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2p6p.cif.gz | 159.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p6p.ent.gz | 128.5 KB | Display | PDB format |
PDBx/mmJSON format | 2p6p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p6/2p6p ftp://data.pdbj.org/pub/pdb/validation_reports/p6/2p6p | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 41409.289 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces fradiae (bacteria) / Strain: Streptomyces fradiae Tue2717 / Gene: urdGT2 / Plasmid: pRSET / Production host: Escherichia coli (E. coli) / Strain (production host): E. coli BL21 (DE3) pLysS / References: UniProt: Q9RPA7 #2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 0.1M HEPES,18% PEG 1500, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.88→68.04 Å / Num. all: 57551 / Num. obs: 57345 / % possible obs: 99.6 % / Redundancy: 4.8 % / Biso Wilson estimate: 29.84 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 6.4 / Net I/σ(I): 15.7 | ||||||||||||||||||
Reflection shell | Resolution: 1.9→68 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 15.7 / Num. unique all: 57346 / Rsym value: 6.4 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.88→68.04 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 7.507 / SU ML: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.149 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.096 Å2
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Refinement step | Cycle: LAST / Resolution: 1.88→68.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.88→1.929 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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