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Yorodumi- PDB-8h1i: Crystal structure of PlyGRCS, a bacteriophage Endolysin in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8h1i | ||||||
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Title | Crystal structure of PlyGRCS, a bacteriophage Endolysin in complex with Cold shock protein C | ||||||
Components |
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Keywords | ANTIMICROBIAL PROTEIN / Endolysin / Bacteriophage / MRSA / Enzybiotic / CspC interactor | ||||||
Function / homology | Function and homology information negative regulation of termination of DNA-templated transcription / transcription antitermination factor activity, RNA binding / single-stranded DNA binding / cellular response to heat / protein-folding chaperone binding / regulation of gene expression / nucleic acid binding / protein homodimerization activity / RNA binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Staphylococcus phage GRCS (virus) Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Padmanabhan, B. / Gopinatha, K. / Mandal, M. / Saranya, G. / Sudhagar, B. | ||||||
Funding support | India, 1items
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Citation | Journal: To Be Published Title: Crystal structure of PlyGRCS, a bacteriophage Endolysin in complex with Cold shock protein C Authors: Padmanabhan, B. / Gopinatha, K. / Mandal, M. / Saranya, G. / Sudhagar, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8h1i.cif.gz | 145.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8h1i.ent.gz | 112.3 KB | Display | PDB format |
PDBx/mmJSON format | 8h1i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h1/8h1i ftp://data.pdbj.org/pub/pdb/validation_reports/h1/8h1i | HTTPS FTP |
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-Related structure data
Related structure data | 4cshS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28549.617 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus phage GRCS (virus) / Gene: GRCS_0015 / Plasmid: pBAD24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon Plus / References: UniProt: W6EBY7 |
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#2: Protein | Mass: 7410.331 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: cspC, msmB, b1823, JW1812 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon plus / References: UniProt: P0A9Y6 |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-MES / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 37.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 50 mM MES, pH 6.0, 5 mM CaCl2, 35% PEGMME 5K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97373 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97373 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→55.29 Å / Num. obs: 16495 / % possible obs: 98 % / Redundancy: 4.2 % / CC1/2: 0.97 / Rmerge(I) obs: 0.137 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.1→2.16 Å / Rmerge(I) obs: 0.533 / Num. unique obs: 1318 / CC1/2: 0.37 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4CSH Resolution: 2.1→49.65 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.44 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→49.65 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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