+Open data
-Basic information
Entry | Database: PDB / ID: 4mli | ||||||
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Title | Crystal structure of the SpyTag/SpyCatcher complex | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / Isopeptide bond / SpyCatcher / Protein engineering | ||||||
Function / homology | Function and homology information Fibronectin binding repeat / Collagen-binding surface protein Cna-like, B-type domain / Fibronectin binding repeat / Cna protein B-type domain / Uncharacterised domain CHP03934, TQXA / Thioester domain / Thioester domain / Prealbumin-like fold domain / Prealbumin-like fold domain / Immunoglobulins ...Fibronectin binding repeat / Collagen-binding surface protein Cna-like, B-type domain / Fibronectin binding repeat / Cna protein B-type domain / Uncharacterised domain CHP03934, TQXA / Thioester domain / Thioester domain / Prealbumin-like fold domain / Prealbumin-like fold domain / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Streptococcus pyogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Li, L. / Fierer, J.O. / Rapoport, T.A. / Howarth, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2014 Title: Structural Analysis and Optimization of the Covalent Association between SpyCatcher and a Peptide Tag. Authors: Li, L. / Fierer, J.O. / Rapoport, T.A. / Howarth, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mli.cif.gz | 95.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mli.ent.gz | 72.9 KB | Display | PDB format |
PDBx/mmJSON format | 4mli.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/4mli ftp://data.pdbj.org/pub/pdb/validation_reports/ml/4mli | HTTPS FTP |
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-Related structure data
Related structure data | 4mlsC 2x5pS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 12415.537 Da / Num. of mol.: 2 / Fragment: UNP residues 440-552 / Mutation: E473I, Y508M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: CnaB2, fba2 / Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: Q8G9G1 #2: Protein/peptide | Mass: 1475.773 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized #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: 1.9 Å3/Da / Density % sol: 35.2 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: Sodium Acetate 0.1M pH4.5, PEG3350 30%, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 11, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 11842 / Num. obs: 9604 / % possible obs: 81.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.7 % / Biso Wilson estimate: 23.84 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 9.18 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 4.4 / Num. unique all: 510 / Rsym value: 0.208 / % possible all: 86.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2x5p Resolution: 2.1→38.288 Å / SU ML: 0.23 / σ(F): 1.97 / Phase error: 26.19 / 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→38.288 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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