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Yorodumi- PDB-5fq1: Structure of the cytoplasmic PAS domain of the Geobacillus thermo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fq1 | ||||||
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Title | Structure of the cytoplasmic PAS domain of the Geobacillus thermodenitrificans histidine kinase CitA | ||||||
Components | HISTIDINE KINASE | ||||||
Keywords | TRANSFERASE / PAS DOMAIN / CITA / TRANSMEMBRANE SIGNALING | ||||||
Function / homology | Function and homology information histidine kinase / phosphorelay sensor kinase activity / membrane => GO:0016020 / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | GEOBACILLUS THERMODENITRIFICANS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.76 Å | ||||||
Authors | Schomburg, B. / Giller, K. / Becker, S. | ||||||
Citation | Journal: Nat. Methods / Year: 2017 Title: Cryogenic optical localization provides 3D protein structure data with Angstrom resolution. Authors: Weisenburger, S. / Boening, D. / Schomburg, B. / Giller, K. / Becker, S. / Griesinger, C. / Sandoghdar, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fq1.cif.gz | 53.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fq1.ent.gz | 42.6 KB | Display | PDB format |
PDBx/mmJSON format | 5fq1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fq1_validation.pdf.gz | 450.2 KB | Display | wwPDB validaton report |
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Full document | 5fq1_full_validation.pdf.gz | 453.4 KB | Display | |
Data in XML | 5fq1_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 5fq1_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fq/5fq1 ftp://data.pdbj.org/pub/pdb/validation_reports/fq/5fq1 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12444.914 Da / Num. of mol.: 2 / Fragment: CYTOPLASMIC PAS DOMAIN, UNP RESIDUES 200-309 Source method: isolated from a genetically manipulated source Source: (gene. exp.) GEOBACILLUS THERMODENITRIFICANS (bacteria) Description: DSM466 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4IPE6, histidine kinase #2: Chemical | ChemComp-GOL / #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | N-TERMINAL GS IS DUE TO CLONING | |
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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: 1.96 Å3/Da / Density % sol: 37 % / Description: NONE |
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Crystal grow | pH: 4.7 Details: 0.4 M K2HPO4, 1.6 M NAH2PO4, 0.1 M PHOSPHATE-CITRATE, PH 4.7 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97929 | |||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2012 | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.78→37.54 Å / Num. obs: 18999 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 6.34 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.78 | |||||||||||||||
Reflection shell | Resolution: 1.78→1.88 Å / Redundancy: 6.14 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.4 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 1.76→37.54 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.658 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.026 / 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: 29.382 Å2
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Refinement step | Cycle: LAST / Resolution: 1.76→37.54 Å
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Refine LS restraints |
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