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Yorodumi- PDB-1ofn: Purification, crystallisation and preliminary structural studies ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ofn | ||||||
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Title | Purification, crystallisation and preliminary structural studies of dTDP-4-keto-6-deoxy-glucose-5-epimerase (EvaD) from Amycolatopsis orientalis; the fourth enzyme in the dTDP-L-epivancosamine biosynthetic pathway. | ||||||
Components | PCZA361.16 | ||||||
Keywords | ISOMERASE / EPIMERASE / VANCOMYCIN GROUP ANTIBIOTIC / EVAD | ||||||
Function / homology | Function and homology information dTDP-4-dehydrorhamnose 3,5-epimerase activity / dTDP-rhamnose biosynthetic process / extracellular polysaccharide biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | AMYCOLATOPSIS ORIENTALIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Merkel, A.B. / Naismith, J.H. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Purification, Crystallization and Preliminary Structural Studies of Dtdp-4-Keto-6-Deoxy-Glucose-5-Epimerase (Evad) from Amycolatopsis Orientalis, the Fourth Enzyme in the Dtdp-L-Epivancosamine ...Title: Purification, Crystallization and Preliminary Structural Studies of Dtdp-4-Keto-6-Deoxy-Glucose-5-Epimerase (Evad) from Amycolatopsis Orientalis, the Fourth Enzyme in the Dtdp-L-Epivancosamine Biosynthetic Pathway. Authors: Merkel, A.B. / Temple, G.K. / Burkart, M.D. / Losey, H.C. / Beis, K. / Walsh, C.T. / Naismith, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ofn.cif.gz | 185.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ofn.ent.gz | 147.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ofn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ofn_validation.pdf.gz | 450.4 KB | Display | wwPDB validaton report |
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Full document | 1ofn_full_validation.pdf.gz | 455.5 KB | Display | |
Data in XML | 1ofn_validation.xml.gz | 23.8 KB | Display | |
Data in CIF | 1ofn_validation.cif.gz | 35.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/1ofn ftp://data.pdbj.org/pub/pdb/validation_reports/of/1ofn | HTTPS FTP |
-Related structure data
Related structure data | 1dzrS S: Starting model for refinement |
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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
#1: Protein | Mass: 22511.697 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) AMYCOLATOPSIS ORIENTALIS (bacteria) / Strain: COSMID PCZA361(AJ223998) / Description: RECOMBINANT PROTEIN / Plasmid: PET24 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O52806 #2: Chemical | ChemComp-GOL / #3: 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: 2.3 Å3/Da / Density % sol: 46.2 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 8 Details: 25%PEG4K, 100MM MGCL2, 100MM TRIS-HCL, PH8.0, SITTING DROP,, pH 8.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 15, 2001 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DIAMOND MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→57.735 Å / Num. obs: 65259 / % possible obs: 100 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 2.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DZR Resolution: 1.5→57.74 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.979 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.066 / 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: 12.21 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→57.74 Å
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Refine LS restraints |
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