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- PDB-4ct3: Methylmercury chloride derivative structure of the lytic CHAPK do... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ct3 | |||||||||
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Title | Methylmercury chloride derivative structure of the lytic CHAPK domain of the endolysin LysK from Staphylococcus aureus bacteriophage K | |||||||||
![]() | ORF30/ORF32 | |||||||||
![]() | VIRAL PROTEIN / PEPTIDOGLYCAN / PROTEASE | |||||||||
Function / homology | ![]() symbiont-mediated cytolysis of host cell / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / peptidase activity / defense response to bacterium / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Sanz-Gaitero, M. / Keary, R. / Garcia-Doval, C. / Coffey, A. / van Raaij, M.J. | |||||||||
![]() | ![]() Title: Crystal structure of the lytic CHAP(K) domain of the endolysin LysK from Staphylococcus aureus bacteriophage K. Authors: Sanz-Gaitero, M. / Keary, R. / Garcia-Doval, C. / Coffey, A. / van Raaij, M.J. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2013 Title: Crystallization of the Chap Domain of the Endolysin from Staphylococcus Aureus Bacteriophage K. Authors: Sanz-Gaitero, M. / Keary, R. / Garcia-Doval, C. / Coffey, A. / van Raaij, M.J. #2: Journal: Bacteriophage / Year: 2011 Title: In Silico Modeling of the Staphylococcal Bacteriophage-Derived Peptidase Chap(K). Authors: Fenton, M. / Cooney, J.C. / Ross, R.P. / Sleator, R.D. / McAuliffe, O. / O'Mahony, J. / Coffey, A. #3: Journal: Appl.Environ.Microbiol. / Year: 2009 Title: Phage Lysin Lysk Can be Truncated to its Chap Domain and Retain Lytic Activity Against Live Antibiotic-Resistant Staphylococci. Authors: Horgan, M. / O'Flynn, G. / Garry, J. / Cooney, J. / Coffey, A. / Fitzgerald, G.F. / Ross, R.P. / McAuliffe, O. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 167.8 KB | Display | ![]() |
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PDB format | ![]() | 131.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 481.5 KB | Display | ![]() |
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Full document | ![]() | 486.6 KB | Display | |
Data in XML | ![]() | 36 KB | Display | |
Data in CIF | ![]() | 51.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 2 - 165 / Label seq-ID: 2 - 165
NCS ensembles :
NCS oper:
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Components
-Protein , 1 types, 4 molecules EGIK
#1: Protein | Mass: 18825.439 Da / Num. of mol.: 4 / Fragment: CHAPK, RESIDUES 1-165 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 7 types, 796 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/MMC.gif)
![](data/chem/img/HG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/MMC.gif)
![](data/chem/img/HG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EPE / #5: Chemical | ChemComp-CA / #6: Chemical | ChemComp-MMC / #7: Chemical | ChemComp-HG / #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 48 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 25 MM TRIS-HCL, 22%(W/V) PEG 8000, 0.1 M 4-(2- HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID (HEPES)-NAOH PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 3, 2013 Details: HORIZONTAL AND VERTICAL FOCUSSING MIRRORS AND SLITS |
Radiation | Monochromator: SI111 DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8352 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→71.92 Å / Num. obs: 48498 / % possible obs: 64.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.69→1.78 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.8 / % possible all: 10.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 1.69→61.5 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.921 / SU B: 2.913 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 22.28 Å2
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Refinement step | Cycle: LAST / Resolution: 1.69→61.5 Å
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Refine LS restraints |
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