+Open data
-Basic information
Entry | Database: PDB / ID: 4jdn | ||||||
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Title | Secreted Chlamydial Protein PGP3, C-terminal Domain | ||||||
Components | Virulence plasmid protein pGP3-D | ||||||
Keywords | CELL INVASION / virulence factor / secreted protein / chlamydia / inflammatory response / tnf | ||||||
Function / homology | Jelly Rolls - #1340 / Jelly Rolls / Sandwich / Mainly Beta / : / : Function and homology information | ||||||
Biological species | Chlamydia trachomatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Galaleldeen, A. / Taylor, A.B. / Chen, D. / Holloway, S.P. / Zhong, G. / Hart, P.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Structure of the Chlamydia trachomatis immunodominant antigen Pgp3. Authors: Galaleldeen, A. / Taylor, A.B. / Chen, D. / Schuermann, J.P. / Holloway, S.P. / Hou, S. / Gong, S. / Zhong, G. / Hart, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jdn.cif.gz | 94 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jdn.ent.gz | 76.9 KB | Display | PDB format |
PDBx/mmJSON format | 4jdn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/4jdn ftp://data.pdbj.org/pub/pdb/validation_reports/jd/4jdn | HTTPS FTP |
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-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: 15965.795 Da / Num. of mol.: 3 / Fragment: C-terminal domain (unp residues 113-264) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Strain: D-LC / Gene: pgp3 / Plasmid: pAG8H / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D7DHH5 #2: Chemical | ChemComp-K / | #3: Chemical | ChemComp-GOL / | #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: 2.4 Å3/Da / Density % sol: 48.82 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 1.2 M Na/K phosphate , pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 22, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 60439 / % possible obs: 99.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 14.3 Å2 / Rsym value: 0.115 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 4 / Num. unique all: 2999 / Rsym value: 0.436 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→37.598 Å / SU ML: 0.14 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 17.54 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.3 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→37.598 Å
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Refine LS restraints |
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LS refinement shell |
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