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Yorodumi- PDB-2ww5: 3D-structure of the modular autolysin LytC from Streptococcus pne... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ww5 | ||||||
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Title | 3D-structure of the modular autolysin LytC from Streptococcus pneumoniae at 1.6 A resolution | ||||||
Components | 1,4-BETA-N-ACETYLMURAMIDASE | ||||||
Keywords | HYDROLASE / GLYCOSIDASE / CHOLINE-BINDING PROTEIN | ||||||
Function / homology | Function and homology information peptidoglycan beta-N-acetylmuramidase / peptidoglycan beta-N-acetylmuramidase activity / mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity / carbohydrate catabolic process / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity Similarity search - Function | ||||||
Biological species | STREPTOCOCCUS PNEUMONIAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.61 Å | ||||||
Authors | Perez-Dorado, I. / Sanles, R. / Hermoso, J.A. / Gonzalez, A. / Garcia, A. / Garcia, P. / Garcia, J.L. / Menendez, M. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2010 Title: Insights Into Pneumococcal Fratricide from the Crystal Structures of the Modular Killing Factor Lytc. Authors: Perez-Dorado, I. / Gonzalez, A. / Morales, M. / Sanles, R. / Striker, W. / Vollmer, W. / Mobashery, S. / Garcia, J.L. / Garcia, A. / Martinez-Ripoll, M. / Garcia, P. / Hermoso, J.A. #1: Journal: J.Biol.Chem. / Year: 2008 Title: Insights Into the Structure-Function Relationships of Pneumococcal Cell Wall Lysozymes, Lytc and Cpl- 1. Authors: Monterroso, B. / Saiz, J.L. / Garcia, P. / Garcia, J.L. / Menendez, M. #2: Journal: Biochem.J. / Year: 2005 Title: Unravelling the Structure of the Pneumococcal Autolytic Lysozyme. Authors: Monterroso, B. / Lopez-Zumel, C. / Garcia, J.L. / Saiz, J.L. / Garcia, P. / Campillo, N.E. / Menendez, M. #3: Journal: Mol.Microbiol. / Year: 1999 Title: The Molecular Characterization of the First Autolytic Lysozyme of Streptococcus Pneumoniae Reveals Evolutionary Mobile Domains. Authors: Garcia, P. / Paz Gonzalez, M. / Garcia, E. / Garcia, J.L. / Lopez, R. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AL" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AL" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ww5.cif.gz | 118.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ww5.ent.gz | 92.1 KB | Display | PDB format |
PDBx/mmJSON format | 2ww5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ww/2ww5 ftp://data.pdbj.org/pub/pdb/validation_reports/ww/2ww5 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 55270.633 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: R6 / Plasmid: PLCC14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9Z4J8, UniProt: Q8DP07*PLUS, lysozyme | ||||||||
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#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-CHT / #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | ENTRY ACCESSION CODE CORRESPONDS TO THE IMMATURE PROTEIN WHICH POSSESSES A SIGNAL PEPTIDE OF 33 ...ENTRY ACCESSION CODE CORRESPOND | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.1 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.98 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 2, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.61→72.93 Å / Num. obs: 76161 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.61→1.7 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2 / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.61→72.93 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.081 / SU ML: 0.056 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. MODEL WAS SUBJECTED TO A FINAL CYCLE OF REFINEMENT USING REFMAC5 WITH TLS. THE FIRST 37 AMINO- ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. MODEL WAS SUBJECTED TO A FINAL CYCLE OF REFINEMENT USING REFMAC5 WITH TLS. THE FIRST 37 AMINO-ACIDS OF THE POLYPEPTIDE CHAIN WERE NOT MODELLED DUE TO THEY WERE NOT VISIBLE IN THE ELECTRON DENSITY MAP.
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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: 23.242 Å2
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Refinement step | Cycle: LAST / Resolution: 1.61→72.93 Å
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Refine LS restraints |
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