+Open data
-Basic information
Entry | Database: PDB / ID: 4mls | ||||||
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Title | Crystal structure of the SpyTag and SpyCatcher-deltaN1 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: 1.984 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 | 4mls.cif.gz | 51.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mls.ent.gz | 36.6 KB | Display | PDB format |
PDBx/mmJSON format | 4mls.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mls_validation.pdf.gz | 428.1 KB | Display | wwPDB validaton report |
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Full document | 4mls_full_validation.pdf.gz | 428.1 KB | Display | |
Data in XML | 4mls_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | 4mls_validation.cif.gz | 8.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/4mls ftp://data.pdbj.org/pub/pdb/validation_reports/ml/4mls | HTTPS FTP |
-Related structure data
Related structure data | 4mliC 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 10192.143 Da / Num. of mol.: 1 / Fragment: UNP residues 461-552 / 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 |
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#2: Protein/peptide | Mass: 1475.773 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.77 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: Sodium Acetate 0.1M pH4.5, NaCl 200mM, PEG3350 30%, Glycerol 5%, VAPOR DIFFUSION, HANGING DROP, temperature 295KK |
-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: 1.984→50 Å / Num. all: 5858 / Num. obs: 5530 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 5.2 / Num. unique all: 281 / Rsym value: 0.362 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2X5P Resolution: 1.984→39.394 Å / SU ML: 0.3 / σ(F): 1.41 / Phase error: 31.25 / 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: 1.984→39.394 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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