+Open data
-Basic information
Entry | Database: PDB / ID: 6sbx | ||||||
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Title | CdbA Form Two | ||||||
Components | CdbA | ||||||
Keywords | DNA BINDING PROTEIN / nucleoid ribbon-helix-helix | ||||||
Function / homology | MXAN_4361/MXAN_4362 family small protein / TIGR04563 family protein Function and homology information | ||||||
Biological species | Myxococcus xanthus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.33 Å | ||||||
Authors | Lovering, A.L. / Cadby, I.T. | ||||||
Citation | Journal: Nat Commun / Year: 2020 Title: CdbA is a DNA-binding protein and c-di-GMP receptor important for nucleoid organization and segregation in Myxococcus xanthus. Authors: Skotnicka, D. / Steinchen, W. / Szadkowski, D. / Cadby, I.T. / Lovering, A.L. / Bange, G. / Sogaard-Andersen, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6sbx.cif.gz | 81 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sbx.ent.gz | 62.1 KB | Display | PDB format |
PDBx/mmJSON format | 6sbx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sb/6sbx ftp://data.pdbj.org/pub/pdb/validation_reports/sb/6sbx | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / Refine code: 0
NCS ensembles :
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-Components
#1: Protein | Mass: 7964.869 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Myxococcus xanthus (bacteria) / Gene: MXAN_4361 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1D489 |
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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: 2.52 Å3/Da / Density % sol: 51.21 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M Na malonate pH 7 0.1M Hepes 30% polyacrylate 2100 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 1, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.33→49.47 Å / Num. obs: 10699 / % possible obs: 99.4 % / Redundancy: 23.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.019 / Rrim(I) all: 0.09 / Net I/σ(I): 17.5 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.33→49.47 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.961 / SU B: 22.909 / SU ML: 0.226 / SU R Cruickshank DPI: 0.2838 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.284 / ESU R Free: 0.217 Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 1.2 Å / Shrinkage radii: 1.2 Å / VDW probe radii: 1.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 184.1 Å2 / Biso mean: 99.728 Å2 / Biso min: 54.84 Å2
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Refinement step | Cycle: final / Resolution: 2.33→49.47 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.33→2.391 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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