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Yorodumi- PDB-2c0z: The 1.6 A resolution crystal structure of NovW: a 4-keto-6-deoxy ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c0z | ||||||
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Title | The 1.6 A resolution crystal structure of NovW: a 4-keto-6-deoxy sugar epimerase from the novobiocin biosynthetic gene cluster of Streptomyces spheroides | ||||||
Components | NOVW | ||||||
Keywords | ISOMERASE / EPIMERASE / ANTIBIOTIC BIOSYNTHESIS / RMLC-LIKE CUPIN | ||||||
Function / homology | Function and homology information novobiocin biosynthetic process / Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives / dTDP-4-dehydrorhamnose 3,5-epimerase activity / isomerase activity Similarity search - Function | ||||||
Biological species | STREPTOMYCES NIVEUS NCIMB 11891 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Jakimowicz, P. / Tello, M. / Freel-Meyers, C.L. / Walsh, C.T. / Buttner, M.J. / Field, R.A. / Lawson, D.M. | ||||||
Citation | Journal: Proteins / Year: 2006 Title: The 1.6 A Resolution Crystal Structure of Novw: A 4-Keto-6-Deoxy Sugar Epimerase from the Novobiocin Biosynthetic Gene Cluster of Streptomyces Spheroides Authors: Jakimowicz, P. / Tello, M. / Freel-Meyers, C.L. / Walsh, C.T. / Buttner, M.J. / Field, R.A. / Lawson, D.M. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Crystallization and Preliminary X-Ray Studies on the Putative Dtdp Sugar Epimerase Novw from the Novobiocin Biosynthetic Cluster of Streptomyces Spheroides Authors: Jakimowicz, P. / Freel-Meyers, C.L. / Walsh, C.T. / Buttner, M.J. / Lawson, D.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c0z.cif.gz | 96.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c0z.ent.gz | 73.3 KB | Display | PDB format |
PDBx/mmJSON format | 2c0z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c0/2c0z ftp://data.pdbj.org/pub/pdb/validation_reports/c0/2c0z | HTTPS FTP |
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-Related structure data
Related structure data | 1ep0S 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: 23204.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES NIVEUS NCIMB 11891 (bacteria) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: Q9L9E5 | ||||
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#2: Chemical | ChemComp-SO4 / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | RESIDUES -8 TO 0 ARE THE EXPRESSION | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 36.7 % |
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Crystal grow | pH: 8.5 Details: 25% SATURATED AMMONIUM SULFATE IN 100MM TRIS-HCL PH8.5, pH 8.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 25, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→39 Å / Num. obs: 26449 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 5.8 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 25.7 |
Reflection shell | Resolution: 1.6→1.64 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.9 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EP0 Resolution: 1.6→51.99 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.241 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.083 / 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: 17.6 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→51.99 Å
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Refine LS restraints |
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