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Yorodumi- PDB-2x8r: The structure of a family GH25 lysozyme from Aspergillus fumigatus -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x8r | ||||||
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Title | The structure of a family GH25 lysozyme from Aspergillus fumigatus | ||||||
Components | GLYCOSYL HYDROLASEGlycoside hydrolase | ||||||
Keywords | HYDROLASE / PEPTIDOGLYCAN CLEAVAGE / ENDO-N-ACETYLMURAMIDASES / DXE MOTIF | ||||||
Function / homology | Function and homology information : / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme activity Similarity search - Function | ||||||
Biological species | ASPERGILLUS FUMIGATUS (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Korczynska, J.E. / Danielsen, S. / Schagerlof, U. / Turkenburg, J.P. / Davies, G.J. / Wilson, K.S. / Taylor, E.J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2010 Title: The Structure of a Family Gh25 Lysozyme from Aspergillus Fumigatus Authors: Korczynska, J.E. / Danielsen, S. / Schagerlof, U. / Turkenburg, J.P. / Davies, G.J. / Wilson, K.S. / Taylor, E.J. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" 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. THE SHEETS PRESENTED AS "BA" 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. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN **-STRANDED BARREL THIS IS REPRESENTED BY A -9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -1-STRANDED BARREL THIS IS REPRESENTED BY A 0-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -1-STRANDED BARREL THIS IS REPRESENTED BY A 0-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "FA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -1-STRANDED BARREL THIS IS REPRESENTED BY A 0-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 | 2x8r.cif.gz | 274.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x8r.ent.gz | 224.1 KB | Display | PDB format |
PDBx/mmJSON format | 2x8r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x8/2x8r ftp://data.pdbj.org/pub/pdb/validation_reports/x8/2x8r | HTTPS FTP |
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-Related structure data
Related structure data | 1jfxS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 23384.047 Da / Num. of mol.: 6 / Fragment: RESIDUES 26-235 / Source method: isolated from a natural source / Source: (natural) ASPERGILLUS FUMIGATUS (mold) / Strain: AF293 / References: UniProt: A4DA29, lysozyme #2: Chemical | ChemComp-CL / #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 Å3/Da / Density % sol: 37 % / Description: NONE |
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Crystal grow | pH: 4 Details: 0.1 M MIB SYSTEM (MALONIC ACID, IMIDAZOLE, BORIC ACID SYSTEM) PH 4.0 AND 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 18, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→40.57 Å / Num. obs: 118667 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JFX Resolution: 1.7→81.5 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.209 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. 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: 14.466 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→81.5 Å
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Refine LS restraints |
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