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Yorodumi- PDB-4qo6: Structural studies of CdsD, a structural protein of the Type III ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qo6 | ||||||
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Title | Structural studies of CdsD, a structural protein of the Type III secretion system (TTSS) of Chlamydia trachomatis | ||||||
Components | Adenylate cyclase-like protein | ||||||
Keywords | STRUCTURAL PROTEIN / Membrane protein / Structural protein of the type III secretion system / inner membrane ring of the type III secretion system | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Chlamydia trachomatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.26 Å | ||||||
Authors | Merilainen, G. / Wierenga, R.K. | ||||||
Citation | Journal: Protein Sci. / Year: 2016 Title: The extended structure of the periplasmic region of CdsD, a structural protein of the type III secretion system of Chlamydia trachomatis. Authors: Merilainen, G. / Koski, M.K. / Wierenga, R.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qo6.cif.gz | 57.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qo6.ent.gz | 41.2 KB | Display | PDB format |
PDBx/mmJSON format | 4qo6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qo6_validation.pdf.gz | 448.9 KB | Display | wwPDB validaton report |
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Full document | 4qo6_full_validation.pdf.gz | 449.5 KB | Display | |
Data in XML | 4qo6_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 4qo6_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qo/4qo6 ftp://data.pdbj.org/pub/pdb/validation_reports/qo/4qo6 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24301.592 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Strain: D/UW-3/Cx / Gene: CT_664 / Production host: Escherichia coli (E. coli) / References: UniProt: O84671 | ||||
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#2: Chemical | #3: Chemical | ChemComp-PEG / | #4: 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: 3.01 Å3/Da / Density % sol: 59.08 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 50 mM MES; pH 6.0 - 3 % PEG4000 - 15 % 2-propanol - 50 mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 9, 2013 |
Radiation | Monochromator: yes / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→28.66 Å / Num. all: 14312 / Num. obs: 13969 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.26→2.39 Å / % possible all: 92.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.26→28.66 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.923 / SU B: 6.243 / SU ML: 0.154 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.242 / ESU R Free: 0.205 / 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: 38.091 Å2
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Refinement step | Cycle: LAST / Resolution: 2.26→28.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.258→2.316 Å / Total num. of bins used: 20
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