+Open data
-Basic information
Entry | Database: PDB / ID: 2xga | ||||||
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Title | MTSL spin-labelled Shigella Flexneri Spa15 | ||||||
Components | SURFACE PRESENTATION OF ANTIGENS PROTEIN SPAK | ||||||
Keywords | CHAPERONE / VIRULENCE FACTOR | ||||||
Function / homology | Surface presentation of antigens protein SpaK / Invasion protein B family / Yope Regulator; Chain: A, - #10 / Yope Regulator; Chain: A, / 2-Layer Sandwich / Alpha Beta / Chem-MTN / Surface presentation of antigens protein SpaK Function and homology information | ||||||
Biological species | SHIGELLA FLEXNERI (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Lillington, J.E.D. / Johnson, S. / Lea, S.M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Shigella Flexneri Spa15 Crystal Structure Verified in Solution by Double Electron Electron Resonance. Authors: Lillington, J.E.D. / Lovett, J.E. / Johnson, S. / Roversi, P. / Timmel, C.R. / Lea, S.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xga.cif.gz | 119.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xga.ent.gz | 93.1 KB | Display | PDB format |
PDBx/mmJSON format | 2xga.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xga_validation.pdf.gz | 1010.5 KB | Display | wwPDB validaton report |
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Full document | 2xga_full_validation.pdf.gz | 1007.5 KB | Display | |
Data in XML | 2xga_validation.xml.gz | 13 KB | Display | |
Data in CIF | 2xga_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/2xga ftp://data.pdbj.org/pub/pdb/validation_reports/xg/2xga | HTTPS FTP |
-Related structure data
Related structure data | 1ry9S 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.497819, -0.002596, -0.867277), Vector: |
-Components
#1: Protein | Mass: 17297.688 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: MTSL SPIN LABEL BOUND TO C19 / Source: (gene. exp.) SHIGELLA FLEXNERI (bacteria) / Strain: M90T / Plasmid: PET-28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834-DE3 / References: UniProt: P35530 #2: Chemical | #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: 2.09 Å3/Da / Density % sol: 41 % / Description: NONE |
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Crystal grow | pH: 6 Details: 100 MM GUANIDINIUM CHLORIDE, 100 MM MES PH 6.0, 50 MM AMMONIUM SULPHATE, 5% ETHYLENE GLYCOL |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 30, 2009 Details: KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING |
Radiation | Monochromator: SI (111) DOUBLE CRYSTAL MONOCHROMATOR. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2→51.38 Å / Num. obs: 19266 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 4.4 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RY9 Resolution: 2.3→51.38 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.877 / SU B: 16.907 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.419 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS
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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: 21.956 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→51.38 Å
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Refine LS restraints |
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