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Yorodumi- PDB-2y6p: Evidence for a Two-Metal-Ion-Mechanism in the Kdo- Cytidylyltrans... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2y6p | ||||||
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Title | Evidence for a Two-Metal-Ion-Mechanism in the Kdo- Cytidylyltransferase KdsB | ||||||
Components | 3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / LIPID A | ||||||
Function / homology | Function and homology information 3-deoxy-manno-octulosonate cytidylyltransferase / 3-deoxy-manno-octulosonate cytidylyltransferase activity / CMP-keto-3-deoxy-D-manno-octulosonic acid biosynthetic process / lipopolysaccharide biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | AQUIFEX AEOLICUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.1 Å | ||||||
Authors | Schmidt, H. / Mesters, J.R. / Mamat, U. / Hilgenfeld, R. | ||||||
Citation | Journal: Plos One / Year: 2011 Title: Evidence for a Two-Metal-Ion Mechanism in the Cytidyltransferase Kdsb, an Enzyme Involved in Lipopolysaccharide Biosynthesis. Authors: Schmidt, H. / Mesters, J.R. / Wu, J. / Woodard, R.W. / Hilgenfeld, R. / Mamat, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y6p.cif.gz | 288.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y6p.ent.gz | 247.8 KB | Display | PDB format |
PDBx/mmJSON format | 2y6p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y6/2y6p ftp://data.pdbj.org/pub/pdb/validation_reports/y6/2y6p | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 27213.490 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) AQUIFEX AEOLICUS (bacteria) / Plasmid: PT7-KDSB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 CODONPLUS(DE3) / Variant (production host): PRIL References: UniProt: O66914, 3-deoxy-manno-octulosonate cytidylyltransferase |
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-Non-polymers , 5 types, 204 molecules
#2: Chemical | #3: Chemical | ChemComp-MG / #4: Chemical | #5: Chemical | ChemComp-BME / | #6: 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: 2.57 Å3/Da / Density % sol: 46.9 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: THE DROPS CONTAINED EQUAL AMOUNTS OF KDSB (10 MG/ML IN 20 MM TRIS-HCL, PH 7.5, 100 MM NACL, 5 MM MGCL2, 2 MM 2-MERCAPTOETHANOL, SUPPLEMENTED WITH 1 MM CTP) AND RESERVOIR SOLUTION (0.1 M ...Details: THE DROPS CONTAINED EQUAL AMOUNTS OF KDSB (10 MG/ML IN 20 MM TRIS-HCL, PH 7.5, 100 MM NACL, 5 MM MGCL2, 2 MM 2-MERCAPTOETHANOL, SUPPLEMENTED WITH 1 MM CTP) AND RESERVOIR SOLUTION (0.1 M HEPES PH 7.5, 18.8% ISOPROPANOL, 18.7% PEG 4000). |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.834 |
Detector | Type: MARRESEARCH SX-165 / Detector: CCD / Date: Sep 14, 2003 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.834 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→29.36 Å / Num. obs: 46213 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 3.75 % / Biso Wilson estimate: 31.9 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.74 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 6.12 / % possible all: 88.5 |
-Processing
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Refinement | Method to determine structure: MIRAS Starting model: NONE Resolution: 2.1→29.35 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.912 / SU B: 12.128 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.264 / ESU R Free: 0.213 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.206 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→29.35 Å
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