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Yorodumi- PDB-4usx: The Structure of the C-terminal YadA-like domain of BPSL2063 from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4usx | ||||||
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Title | The Structure of the C-terminal YadA-like domain of BPSL2063 from Burkholderia pseudomallei | ||||||
Components | TRIMERIC AUTOTRANSPORTER ADHESIN | ||||||
Keywords | TRANSPORT PROTEIN / YADA-LIKE HEAD DOMAIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | BURKHOLDERIA PSEUDOMALLEI K96243 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Perletti, L. / Gourlay, L.J. / Peano, C. / Pietrelli, A. / DeBellis, G. / Deantonio, C. / Santoro, C. / Sblattero, D. / Bolognesi, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Selecting Soluble/Foldable Protein Domains Through Single-Gene or Genomic Orf Filtering: Structure of the Head Domain of Burkholderia Pseudomallei Antigen Bpsl2063. Authors: Gourlay, L.J. / Peano, C. / Deantonio, C. / Perletti, L. / Pietrelli, A. / Villa, R. / Matterazzo, E. / Lassaux, P. / Santoro, C. / Puccio, S. / Sblattero, D. / Bolognesi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4usx.cif.gz | 136.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4usx.ent.gz | 102.1 KB | Display | PDB format |
PDBx/mmJSON format | 4usx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/us/4usx ftp://data.pdbj.org/pub/pdb/validation_reports/us/4usx | HTTPS FTP |
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-Related structure data
Related structure data | 3laaS 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:
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-Components
#1: Protein | Mass: 35838.844 Da / Num. of mol.: 3 Fragment: YADA-LIKE COLLAGEN BINDING DOMAIN, UNP RESIDUES 657-992 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BURKHOLDERIA PSEUDOMALLEI K96243 (bacteria) Plasmid: PET21B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): STAR / References: UniProt: Q63TA4 #2: Chemical | ChemComp-MG / #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: 2.18 Å3/Da / Density % sol: 43.74 % / Description: NONE |
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Crystal grow | pH: 4 Details: PACT PREMIER (MOLECULAR DIMENSIONS) CONDITION D1 (0.1M MALIC ACID, MES AND TRIS (MMT) BUFFER PH 4.0, 25% PEG1500. CRYSTALS WERE CRYOCOOLED IN MOTHER LIQUOR CONTAINING 40% PEG1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 27, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8729 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. obs: 48598 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Biso Wilson estimate: 15.35 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.9 / % possible all: 93.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3LAA Resolution: 1.8→39.69 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 21.47 / Stereochemistry target values: ML Details: PROTEOLYSIS OCCURRED DURING RESULTING IN THE LOSS OF APPROX 136 C-TERMINAL RESIDUES
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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: 1.8→39.69 Å
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Refine LS restraints |
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LS refinement shell |
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