+Open data
-Basic information
Entry | Database: PDB / ID: 2xi9 | ||||||
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Title | Pilus-presented adhesin, Spy0125 (Cpa), P1 form | ||||||
Components | ANCILLARY PROTEIN 1 | ||||||
Keywords | CELL ADHESION / GRAM POSITIVE PILUS / INTRAMOLECULAR ISOPEPTIDE BOND / INTERNAL THIOESTER | ||||||
Function / homology | Function and homology information | ||||||
Biological species | STREPTOCOCCUS PYOGENES (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | Pointon, J.A. / Smith, W.D. / Saalbach, G. / Crow, A. / Kehoe, M.A. / Banfield, M.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: A Highly Unusual Thioester Bond in a Pilus Adhesin is Required for Efficient Host Cell Interaction Authors: Pointon, J.A. / Smith, W.D. / Saalbach, G. / Crow, A. / Kehoe, M.A. / Banfield, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xi9.cif.gz | 278.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xi9.ent.gz | 232.2 KB | Display | PDB format |
PDBx/mmJSON format | 2xi9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xi/2xi9 ftp://data.pdbj.org/pub/pdb/validation_reports/xi/2xi9 | 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: 51475.434 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, RESIDUES 286-723 Source method: isolated from a genetically manipulated source Details: INTERNAL THIOESTER LINKAGE BETWEEN CYS426 AND GLN575. INTRAMOLECULAR ISOPEPTIDE BOND BETWEEN LYS297 AND ASP595. INTRAMOLECULAR ISOPEPTIDE BOND BETWEEN LYS610 AND ASN715. Source: (gene. exp.) STREPTOCOCCUS PYOGENES (bacteria) / Strain: SF370 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8GRA2 #2: 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: 2.36 Å3/Da / Density % sol: 48 % / Description: NONE |
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Crystal grow | pH: 5.75 Details: 38 - 40 % PEG 4000, 200 MM SODIUM ACETATE AND 100 MM TRI-SODIUM CITRATE PH 5.6 - 5.9; 34 TO 36 % PEG 5000-MME, 100 MM AMMONIUM SULPHATE, 100 MM MES PH 6.0 - 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9785 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 13, 2009 / Details: MIRROS |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→38 Å / Num. obs: 66113 / % possible obs: 93.6 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 5 / % possible all: 74.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 1.9→34.11 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.904 / SU B: 5.937 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CA 120 RESIDUES AT C_TERMINUS ARE DISORDERED. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CA 120 RESIDUES AT C_TERMINUS ARE DISORDERED. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. ATOM AND ANISO RECORDS BELOW CONTAIN THE SUM OF TLS AND RESIDUAL B/U FACTORS, AS OUPUT FROM REFMAC5 USING THE 'TLSO ADDU' OPTION. WATERS HAVE BEEN INCLUDED IN THE TLS REFINEMENT, BUT TO WHICH GROUP THEY HAVE BEEN ASSIGNED IS UNKNOWN.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.65 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→34.11 Å
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Refine LS restraints |
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