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- PDB-3tqd: Structure of the 3-deoxy-D-manno-octulosonate cytidylyltransferas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3tqd | ||||||
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Title | Structure of the 3-deoxy-D-manno-octulosonate cytidylyltransferase (kdsB) from Coxiella burnetii | ||||||
![]() | 3-deoxy-manno-octulosonate cytidylyltransferase | ||||||
![]() | TRANSFERASE / Cell envelope | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Franklin, M.C. / Cheung, J. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J. | ||||||
![]() | ![]() Title: Structural genomics for drug design against the pathogen Coxiella burnetii. Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116.6 KB | Display | ![]() |
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PDB format | ![]() | 89.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.1 KB | Display | ![]() |
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Full document | ![]() | 443 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 18.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3tq8C ![]() 3tq9C ![]() 3tqaC ![]() 3tqbC ![]() 3tqcC ![]() 3tqeC ![]() 3tqfC ![]() 3tqgC ![]() 3tqhC ![]() 3tqiC ![]() 3tqjC ![]() 3tqlC ![]() 3tqmC ![]() 3tqnC ![]() 3tqoC ![]() 3tqpC ![]() 3tqqC ![]() 3tqrC ![]() 3tqsC ![]() 3tqtC ![]() 3tquC ![]() 3tqwC ![]() 3tqxC ![]() 3tqyC ![]() 3tqzC ![]() 3tr0C ![]() 3tr1C ![]() 3tr2C ![]() 3tr3C ![]() 3tr4C ![]() 3tr5C ![]() 3tr6C ![]() 3tr7C ![]() 3tr8C ![]() 3tr9C ![]() 3trbC ![]() 3trcC ![]() 3trdC ![]() 3treC ![]() 3trfC ![]() 3trgC ![]() 3trhC ![]() 3triC ![]() 3tthC ![]() 3ty2C ![]() 3uwcC ![]() 4f3qC ![]() 4f3rC ![]() 4nbqC ![]() 4ng4C ![]() 3k8dS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29089.027 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q83E52, 3-deoxy-manno-octulosonate cytidylyltransferase |
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#2: Chemical | ChemComp-NI / |
#3: Chemical | ChemComp-ACT / |
#4: Water | ChemComp-HOH / |
Sequence details | RESIDUES -3 TO 0 REPRESENT AN INCORRECTL |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.17 M ammonium acetate, 0.085 M Na citrate, 25.5% PEG 4000, 15% glycerol, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 15, 2011 |
Radiation | Monochromator: VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→100 Å / Num. all: 23582 / Num. obs: 23093 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.9 % / Rsym value: 0.053 / Net I/σ(I): 39.4 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 1186 / Rsym value: 0.454 / % possible all: 88 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3K8D Resolution: 1.8→25.62 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 6.379 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.131 / 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: 39.645 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→25.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.845 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -5.344 Å / Origin y: 42.4897 Å / Origin z: 17.326 Å
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