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Yorodumi- PDB-5xgb: Crystal structure of the PAS-GGDEF-EAL domain of PA0861 from Pseu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xgb | ||||||
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Title | Crystal structure of the PAS-GGDEF-EAL domain of PA0861 from Pseudomonas aeruginosa | ||||||
Components | Uncharacterized protein | ||||||
Keywords | TRANSCRIPTION / PAS domain / GGDEF-EAL domain / Pseudomonas aeruginosa / Biofilm / RbdA / PA0861 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.28 Å | ||||||
Authors | Liu, C. / Liew, C.W. / Sreekanth, R. / Lescar, J. | ||||||
Citation | Journal: J. Bacteriol. / Year: 2018 Title: Insights into Biofilm Dispersal Regulation from the Crystal Structure of the PAS-GGDEF-EAL Region of RbdA from Pseudomonas aeruginosa. Authors: Liu, C. / Liew, C.W. / Wong, Y.H. / Tan, S.T. / Poh, W.H. / Manimekalai, M.S.S. / Rajan, S. / Xin, L. / Liang, Z.X. / Gruber, G. / Rice, S.A. / Lescar, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xgb.cif.gz | 235.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xgb.ent.gz | 188.7 KB | Display | PDB format |
PDBx/mmJSON format | 5xgb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/5xgb ftp://data.pdbj.org/pub/pdb/validation_reports/xg/5xgb | 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: 63485.305 Da / Num. of mol.: 1 / Fragment: UNP residues 233-800 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: PA0861 / Plasmid: pNIC-CH2 / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta DE3 / References: UniProt: Q9I580 |
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#2: 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: 2.89 Å3/Da / Density % sol: 57.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M MES/imidazole at pH 6.5, 0.1 M carboxylic acid, 10% (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→70.2 Å / Num. obs: 33717 / % possible obs: 100 % / Redundancy: 6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.054 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.28→2.4 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.06 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4851 / CC1/2: 0.517 / Rpim(I) all: 0.454 / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 2.28→70.15 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.91 / SU R Cruickshank DPI: 0.242 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.252 / SU Rfree Blow DPI: 0.194 / SU Rfree Cruickshank DPI: 0.193
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Displacement parameters | Biso mean: 52.09 Å2
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Refine analyze | Luzzati coordinate error obs: 0.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.28→70.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.28→2.35 Å / Total num. of bins used: 17
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Refinement TLS params. | Method: refined / Origin x: 40.1164 Å / Origin y: 0.8088 Å / Origin z: 91.2216 Å
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Refinement TLS group | Selection details: { A|* } |