+Open data
-Basic information
Entry | Database: PDB / ID: 4arq | ||||||
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Title | Structure of the pesticin S89C, S285C double mutant | ||||||
Components | (PESTICIN) x 2 | ||||||
Keywords | HYDROLASE / MURAMIDASE | ||||||
Function / homology | Function and homology information metabolic process / lysozyme activity / killing of cells of another organism / defense response to bacterium Similarity search - Function | ||||||
Biological species | YERSINIA PESTIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Zeth, K. / Patzer, S.I. / Albrecht, R. / Braun, V. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Structure and Mechanistic Studies of Pesticin, a Bacterial Homolog of Phage Lysozymes. Authors: Patzer, S.I. / Albrecht, R. / Braun, V. / Zeth, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4arq.cif.gz | 281.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4arq.ent.gz | 230.3 KB | Display | PDB format |
PDBx/mmJSON format | 4arq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ar/4arq ftp://data.pdbj.org/pub/pdb/validation_reports/ar/4arq | HTTPS FTP |
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-Related structure data
Related structure data | 4aqnSC 4arjC 4arlC 4armC 4arpC 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 40122.043 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) YERSINIA PESTIS (bacteria) / Plasmid: T7, PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q57159 |
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#2: Protein | Mass: 40123.027 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) YERSINIA PESTIS (bacteria) / Plasmid: T7, PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q57159 |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
Compound details | ENGINEERED RESIDUE IN CHAIN A, SER 89 TO CYS ENGINEERED RESIDUE IN CHAIN A, SER 285 TO CYS ...ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.32 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 25% PEG8000, 0.2M MGCL2, 0.1M HEPES PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→36 Å / Num. obs: 22615 / % possible obs: 97.7 % / Observed criterion σ(I): 3.3 / Redundancy: 2.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.6→2.76 Å / Redundancy: 97.8 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 2.2 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AQN Resolution: 2.6→36.521 Å / SU ML: 0.33 / σ(F): 1.32 / Phase error: 29.89 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.444 Å2 / ksol: 0.287 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.6→36.521 Å
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Refine LS restraints |
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LS refinement shell |
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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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