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Yorodumi- PDB-3i6b: Crystal structure of YrbI lacking the last 8 residues, in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3i6b | ||||||
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Title | Crystal structure of YrbI lacking the last 8 residues, in complex with Kdo and inorganic phosphate | ||||||
Components | 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase | ||||||
Keywords | HYDROLASE / YrbI / KdsC / Kdo / phosphatase / Lipopolysaccharide biosynthesis / Magnesium | ||||||
Function / homology | Function and homology information 3-deoxy-manno-octulosonate-8-phosphatase / 3-deoxy-manno-octulosonate-8-phosphatase activity / lipopolysaccharide biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å | ||||||
Authors | Biswas, T. / Tsodikov, O.V. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: The Tail of KdsC: CONFORMATIONAL CHANGES CONTROL THE ACTIVITY OF A HALOACID DEHALOGENASE SUPERFAMILY PHOSPHATASE. Authors: Biswas, T. / Yi, L. / Aggarwal, P. / Wu, J. / Rubin, J.R. / Stuckey, J.A. / Woodard, R.W. / Tsodikov, O.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3i6b.cif.gz | 142.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i6b.ent.gz | 112.1 KB | Display | PDB format |
PDBx/mmJSON format | 3i6b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/3i6b ftp://data.pdbj.org/pub/pdb/validation_reports/i6/3i6b | HTTPS FTP |
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-Related structure data
Related structure data | 2r8eSC 2r8xC 2r8yC 2r8zC 3hycC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 19206.242 Da / Num. of mol.: 4 / Fragment: Residues 1-180 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: B / Gene: c3958, kdsC, YrbI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P67653, 3-deoxy-manno-octulosonate-8-phosphatase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-PO4 / #4: Sugar | #5: 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: 2.22 Å3/Da / Density % sol: 44.64 % |
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Crystal grow | Temperature: 294 K / pH: 6.5 Details: 1.875 M Ammonium Sulfate, 100mM Na Cacodylate pH 6.5, 2.5% glycerol, stoichiometric amount of Kdo8P (cleaved upon incubation in the drop), VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.06699 |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 6, 2007 |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.06699 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→50 Å / Num. obs: 21494 / % possible obs: 92.7 % / Observed criterion σ(I): 2.3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.49→2.65 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.3 / % possible all: 94.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB CODE: 2R8E Resolution: 2.49→40 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.899 / SU B: 20.357 / SU ML: 0.225 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.312 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.34 Å2
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Refinement step | Cycle: LAST / Resolution: 2.49→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.49→2.55 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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