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Yorodumi- PDB-3tqc: Structure of the pantothenate kinase (coaA) from Coxiella burnetii -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tqc | ||||||
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Title | Structure of the pantothenate kinase (coaA) from Coxiella burnetii | ||||||
Components | Pantothenate kinase | ||||||
Keywords | TRANSFERASE / Biosynthesis of cofactors / prosthetic groups / carriers | ||||||
Function / homology | Function and homology information pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / kinase activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Coxiella burnetii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Franklin, M.C. / Cheung, J. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J. | ||||||
Citation | Journal: Proteins / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tqc.cif.gz | 270 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tqc.ent.gz | 217.8 KB | Display | PDB format |
PDBx/mmJSON format | 3tqc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tqc_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3tqc_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3tqc_validation.xml.gz | 28.3 KB | Display | |
Data in CIF | 3tqc_validation.cif.gz | 40.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tq/3tqc ftp://data.pdbj.org/pub/pdb/validation_reports/tq/3tqc | HTTPS FTP |
-Related structure data
Related structure data | 3tq8C 3tq9C 3tqaC 3tqbC 3tqdC 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 1esmS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 4
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-Components
#1: Protein | Mass: 37238.742 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA 493 Nine Mile Phase I / Gene: CBU_0199, coaA / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83EV9, pantothenate kinase #2: Chemical | #3: 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: 2.91 Å3/Da / Density % sol: 57.69 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: 0.2 M sodium chloride, 10% PEG8000, 0.1 M CHES, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 29, 2011 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→100 Å / Num. all: 51888 / Num. obs: 46728 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Rsym value: 0.062 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 4.5 / Num. unique all: 2552 / Rsym value: 0.306 / % possible all: 91 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB CODE 1ESM Resolution: 2.3→72.33 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.889 / SU B: 13.799 / SU ML: 0.154 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.339 / ESU R Free: 0.258 / 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: 30.956 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→72.33 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4263 / Refine-ID: X-RAY DIFFRACTION / Rms dev position: 0.37 Å
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LS refinement shell | Resolution: 2.3→2.36 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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