+Open data
-Basic information
Entry | Database: PDB / ID: 1oi6 | ||||||
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Title | Structure determination of the TMP-complex of EvaD | ||||||
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: 1.4 Å | ||||||
Authors | Merkel, A.B. / Naismith, J.H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: The Position of a Key Tyrosine in Dtdp-4-Keto-6-Deoxy-D-Glucose-5-Epimerase (Evad) Alters the Substrate Profile for This Rmlc-Like Enzyme Authors: Merkel, A.B. / Major, L.L. / Errey, J.C. / Burkart, M.D. / Field, R.A. / Walsh, C.T. / Naismith, J.H. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Purification, Crystallisation and Preliminary Structural Studies of Dtdp-4-Keto-6-Deoxy-Glucose-5-Epimerase (Evad) from Amycolatpsis Orientalis; the Fourth Enzyme in the Dtdp-L-Epivancosamine Pathway Authors: Merkel, A.B. / Temple, G.K. / Burkhart, M. / 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 | 1oi6.cif.gz | 196 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oi6.ent.gz | 155.1 KB | Display | PDB format |
PDBx/mmJSON format | 1oi6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/1oi6 ftp://data.pdbj.org/pub/pdb/validation_reports/oi/1oi6 | HTTPS FTP |
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-Related structure data
Related structure data | 1ofnS 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: PCZA361(AJ223998) / Plasmid: PET24 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O52806 #2: Chemical | #3: Chemical | #4: 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 29, 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: 1.4→34.1 Å / Num. obs: 80059 / % possible obs: 99.8 % / Redundancy: 4 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 4 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.5 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OFN Resolution: 1.4→34.1 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.731 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.053 / 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: 11.56 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→34.1 Å
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Refine LS restraints |
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