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- PDB-3g9k: Crystal structure of Bacillus anthracis transpeptidase enzyme CapD -
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Open data
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Basic information
Entry | Database: PDB / ID: 3g9k | ||||||
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Title | Crystal structure of Bacillus anthracis transpeptidase enzyme CapD | ||||||
![]() | (Capsule biosynthesis protein capD) x 2 | ||||||
![]() | HYDROLASE / CapD protein / Bacillus anthracis / The Great Lakes Regional Center of Excellence / GLRCE / Capsule biogenesis/degradation / Virulence | ||||||
Function / homology | ![]() capsule polysaccharide biosynthetic process / Transferases; Acyltransferases; Aminoacyltransferases / peptidase activity / transferase activity / proteolysis Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, R. / Wu, R. / Richter, S. / Anderson, V.J. / Missiakas, D. / Joachimiak, A. | ||||||
![]() | ![]() Title: Crystal Structure of Bacillus anthracis Transpeptidase Enzyme CapD. Authors: Wu, R. / Richter, S. / Zhang, R.G. / Anderson, V.J. / Missiakas, D. / Joachimiak, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 198.2 KB | Display | ![]() |
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PDB format | ![]() | 156.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 472.6 KB | Display | ![]() |
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Full document | ![]() | 489.7 KB | Display | |
Data in XML | ![]() | 39.7 KB | Display | |
Data in CIF | ![]() | 58.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ga9SC 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36223.242 Da / Num. of mol.: 2 / Fragment: UNP residues 29-351 Source method: isolated from a genetically manipulated source Details: Long chain / Source: (gene. exp.) ![]() ![]() Gene: BAK_B0097, BXB0063, capD, dep, GBAA_pXO2_0063, pXO2-55 Plasmid: pDM68 / Production host: ![]() ![]() #2: Protein | Mass: 19594.777 Da / Num. of mol.: 2 / Fragment: UNP residues 352-528 Source method: isolated from a genetically manipulated source Details: Short chain / Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.12 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 15% PEG 3350, 8% PEG 400, 0.05M LiSO4, 0.1M Na-Hepes pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 19, 2006 / Details: mirrors |
Radiation | Monochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→50 Å / Num. all: 88013 / Num. obs: 83551 / % possible obs: 98 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.79→1.83 Å / Redundancy: 4 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 1.73 / % possible all: 82.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3GA9 Resolution: 1.79→40.69 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.964 / SU ML: 0.096 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.133 / 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: 22.615 Å2
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Refinement step | Cycle: LAST / Resolution: 1.79→40.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.79→1.84 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 14.453 Å / Origin y: -17.479 Å / Origin z: 19.274 Å
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Refinement TLS group |
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