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Yorodumi- PDB-7aqh: Cell wall binding domain of the Staphylococcal phage 2638A endolysin -
+Open data
-Basic information
Entry | Database: PDB / ID: 7aqh | ||||||
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Title | Cell wall binding domain of the Staphylococcal phage 2638A endolysin | ||||||
Components | ORF007 | ||||||
Keywords | VIRAL PROTEIN / Bacteriophage / phage / endolysin / SH3b / cell wall binding domain / staphylococcus | ||||||
Function / homology | Function and homology information cytolysis / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / defense response to bacterium Similarity search - Function | ||||||
Biological species | Staphylococcus phage 2638A (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å | ||||||
Authors | Dunne, M. / Sobieraj, A. / Ernst, P. / Mittl, P.R.E. / Pluckthun, A. / Loessner, M.J. | ||||||
Citation | Journal: To Be Published Title: Cell wall binding domain of the Staphylococcal phage 2638A endolysin Authors: Dunne, M. / Sobieraj, A. / Ernst, P. / Mittl, P.R.E. / Pluckthun, A. / Loessner, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7aqh.cif.gz | 201.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7aqh.ent.gz | 130.5 KB | Display | PDB format |
PDBx/mmJSON format | 7aqh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/7aqh ftp://data.pdbj.org/pub/pdb/validation_reports/aq/7aqh | HTTPS FTP |
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-Related structure data
Related structure data | 5leoS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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7 |
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8 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Beg auth comp-ID: TRP / Beg label comp-ID: TRP / End auth comp-ID: ILE / End label comp-ID: ILE / Auth seq-ID: 393 - 485 / Label seq-ID: 2 - 94
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-Components
#1: Protein | Mass: 10987.453 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus phage 2638A (virus) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4ZD58 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.64 Å3/Da / Density % sol: 53 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: Protein buffer: 20 mM Tris, 150 mM NaCl, pH 7.4 Crystallization buffer: 1% (W/V) tryptone, 0.05 M HEPES, pH 7.0, 12% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 11, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.488→44.11 Å / Num. obs: 51577 / % possible obs: 90.91 % / Redundancy: 2.06 % / Biso Wilson estimate: 51.65 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.077 / Rrim(I) all: 0.117 / Net I/σ(I): 4.31 |
Reflection shell | Resolution: 2.488→2.57 Å / Rmerge(I) obs: 0.678 / Mean I/σ(I) obs: 0.68 / Num. unique obs: 2454 / CC1/2: 0.486 / CC star: 0.809 / Rpim(I) all: 0.598 / Rrim(I) all: 0.907 / % possible all: 79.34 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LEO Resolution: 2.49→44.11 Å / SU ML: 0.4546 / Cross valid method: FREE R-VALUE / σ(F): 1.22 / Phase error: 36.2138 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.73 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.49→44.11 Å
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Refine LS restraints |
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LS refinement shell |
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