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Yorodumi- PDB-5ttd: Minor pilin FctB from S. pyogenes with engineered intramolecular ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ttd | |||||||||
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Title | Minor pilin FctB from S. pyogenes with engineered intramolecular isopeptide bond | |||||||||
Components | Maltose-binding periplasmic protein,Pilin isopeptide linkage domain protein | |||||||||
Keywords | CELL ADHESION / isopeptide bond / protein engineering / autocatalytic reaction | |||||||||
Function / homology | Function and homology information detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / membrane => GO:0016020 / periplasmic space / DNA damage response / membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) Streptococcus pyogenes (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Young, P.G. / Kwon, H. / Squire, C.J. / Baker, E.N. | |||||||||
Funding support | New Zealand, 1items
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Citation | Journal: Sci Rep / Year: 2017 Title: Engineering a Lys-Asn isopeptide bond into an immunoglobulin-like protein domain enhances its stability. Authors: Kwon, H. / Young, P.G. / Squire, C.J. / Baker, E.N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ttd.cif.gz | 185.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ttd.ent.gz | 144.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ttd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tt/5ttd ftp://data.pdbj.org/pub/pdb/validation_reports/tt/5ttd | HTTPS FTP |
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-Related 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: 55110.996 Da / Num. of mol.: 2 / Fragment: UNP residues 33-392,UNP residues 26-148 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Streptococcus pyogenes (bacteria) Plasmid: pPROEX-Hta / Strain: 90/306S / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P0AEY0, UniProt: U2UUZ4, UniProt: P0AEX9*PLUS #2: Polysaccharide | #3: Chemical | ChemComp-FMT / #4: 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: 2.68 Å3/Da / Density % sol: 54.1 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 12.5% PEG 1000, 10% PEG 3350, 12.5% MPD, 0.1M MES/imidazole pH 6.5, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, 0.02 M sodium oxamate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 31, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2→19.57 Å / Num. obs: 78932 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / CC1/2: 0.997 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 1.6 / CC1/2: 0.525 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KLQ and 1ANF Resolution: 2→19.57 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.347 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.681 Å2
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Refinement step | Cycle: 1 / Resolution: 2→19.57 Å
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Refine LS restraints |
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