+Open data
-Basic information
Entry | Database: PDB / ID: 6hbz | ||||||
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Title | Bdellovibrio bacteriovorus DgcB Full-length | ||||||
Components | GGDEF domain protein | ||||||
Keywords | SIGNALING PROTEIN / GGDEF / FHA / c-di-GMP / diguanylate cyclase | ||||||
Function / homology | Function and homology information negative regulation of bacterial-type flagellum-dependent cell motility / diguanylate cyclase activity / cell adhesion involved in single-species biofilm formation / nucleotide binding / plasma membrane Similarity search - Function | ||||||
Biological species | Bdellovibrio bacteriovorus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.79 Å | ||||||
Authors | Lovering, A.L. / Meek, R.W. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Commun / Year: 2019 Title: Structural basis for activation of a diguanylate cyclase required for bacterial predation in Bdellovibrio. Authors: Meek, R.W. / Cadby, I.T. / Moynihan, P.J. / Lovering, A.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hbz.cif.gz | 250.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hbz.ent.gz | 200.2 KB | Display | PDB format |
PDBx/mmJSON format | 6hbz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hb/6hbz ftp://data.pdbj.org/pub/pdb/validation_reports/hb/6hbz | 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:
NCS ensembles :
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-Components
#1: Protein | Mass: 30456.697 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100) (bacteria) Strain: ATCC 15356 / DSM 50701 / NCIB 9529 / HD100 / Gene: Bd0742 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6MPU8 #2: Chemical | #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-EDO / #5: 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 grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.2M KBr, 0.1M sodium acetate, 15% PEG 4000 |
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 13, 2015 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.79→153.09 Å / Num. obs: 97476 / % possible obs: 100 % / Redundancy: 37 % / CC1/2: 0.998 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.02 / Rrim(I) all: 0.123 / Net I/σ(I): 20.4 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→153.09 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 6.706 / SU ML: 0.085 / SU R Cruickshank DPI: 0.1007 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.089 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.3 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 120.04 Å2 / Biso mean: 35.3 Å2 / Biso min: 17.12 Å2
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Refinement step | Cycle: final / Resolution: 1.79→153.09 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: 1.786→1.832 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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