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Yorodumi- PDB-3dfm: The crystal structure of the zinc inhibited form of teicoplanin d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dfm | ||||||
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Title | The crystal structure of the zinc inhibited form of teicoplanin deacetylase Orf2 | ||||||
Components | TEICOPLANIN PSEUDOAGLYCONE DEACETYLASE ORF2 | ||||||
Keywords | HYDROLASE / zinc inhibited binuclear zinc cluster / alpha-beta single domain | ||||||
Function / homology | Function and homology information N-acetylglucosaminylphosphatidylinositol deacetylase activity / glycoside metabolic process / GPI anchor biosynthetic process / acyltransferase activity / glycosyltransferase activity / ligase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Actinoplanes teichomyceticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | ||||||
Authors | Zou, Y. / Brunzelle, J.S. / Nair, S.K. | ||||||
Citation | Journal: Chem.Biol. / Year: 2008 Title: Crystal structures of lipoglycopeptide antibiotic deacetylases: implications for the biosynthesis of a40926 and teicoplanin. Authors: Zou, Y. / Brunzelle, J.S. / Nair, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dfm.cif.gz | 62.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dfm.ent.gz | 49.8 KB | Display | PDB format |
PDBx/mmJSON format | 3dfm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dfm_validation.pdf.gz | 440.7 KB | Display | wwPDB validaton report |
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Full document | 3dfm_full_validation.pdf.gz | 442 KB | Display | |
Data in XML | 3dfm_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 3dfm_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/3dfm ftp://data.pdbj.org/pub/pdb/validation_reports/df/3dfm | 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: 30295.033 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Actinoplanes teichomyceticus (bacteria) Gene: tcp14 / References: UniProt: Q6ZZJ1 | ||||
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#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.08 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9704 Å |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9704 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. obs: 16079 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→25 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.123 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.221 / ESU R Free: 0.182 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.67 Å2
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Refinement step | Cycle: LAST / Resolution: 2.01→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.014→2.066 Å / Total num. of bins used: 20
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