+Open data
-Basic information
Entry | Database: PDB / ID: 6k4f | ||||||
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Title | SiaC of Pseudomonas aeruginosa | ||||||
Components | DUF1987 domain-containing protein | ||||||
Keywords | BIOSYNTHETIC PROTEIN / SiaC / Biofilm | ||||||
Function / homology | SiaC family regulatory phosphoprotein / SiaC family regulatory phosphoprotein / Biofilm formation regulator SiaD modulator protein SiaC / Uncharacterized protein PA14_02130 Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.735 Å | ||||||
Authors | Lin, J.Q. / Lescar, J. | ||||||
Citation | Journal: Plos One / Year: 2020 Title: The SiaABC threonine phosphorylation pathway controls biofilm formation in response to carbon availability in Pseudomonas aeruginosa. Authors: Poh, W.H. / Lin, J. / Colley, B. / Muller, N. / Goh, B.C. / Schleheck, D. / El Sahili, A. / Marquardt, A. / Liang, Y. / Kjelleberg, S. / Lescar, J. / Rice, S.A. / Klebensberger, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k4f.cif.gz | 64.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k4f.ent.gz | 46.3 KB | Display | PDB format |
PDBx/mmJSON format | 6k4f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6k4f_validation.pdf.gz | 424.2 KB | Display | wwPDB validaton report |
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Full document | 6k4f_full_validation.pdf.gz | 424.2 KB | Display | |
Data in XML | 6k4f_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | 6k4f_validation.cif.gz | 9.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/6k4f ftp://data.pdbj.org/pub/pdb/validation_reports/k4/6k4f | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 14786.435 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: SF file contains Friedel pairs. / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: ALP65_03379, CGU42_29970, DT376_26170, DY979_27175, DZ962_26905, EB236_19545, ECC04_17625, EFK27_14525, EFK68_31140, EGJ96_17530, EQH76_15975, IPC24_23845, IPC3_18980, PA34_000955, PAMH19_0166 Production host: Escherichia coli (E. coli) / References: UniProt: A0A072ZHB4, UniProt: Q02UQ8*PLUS |
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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: 2.12 Å3/Da / Density % sol: 41.94 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M phosphate/citrate, PH4.2, 40% (v/v) PEG 300 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 1.735→57.96 Å / Num. obs: 13113 / % possible obs: 98.94 % / Redundancy: 8.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.09846 / Rpim(I) all: 0.03468 / Net I/σ(I): 12.05 |
Reflection shell | Resolution: 1.735→1.797 Å / Rmerge(I) obs: 1.129 / Num. unique obs: 1176 / CC1/2: 0.62 / Rpim(I) all: 0.4561 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.735→57.96 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.44
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.735→57.96 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 14.7126 Å / Origin y: 16.1319 Å / Origin z: 14.027 Å
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Refinement TLS group | Selection details: all |