+Open data
-Basic information
Entry | Database: PDB / ID: 3tvk | ||||||
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Title | Diguanylate cyclase domain of DgcZ | ||||||
Components | Diguanylate cyclase DgcZ | ||||||
Keywords | TRANSFERASE / diguanylate cyclase / putative zinc sensor / c-di-GMP | ||||||
Function / homology | Function and homology information negative regulation of bacterial-type flagellum assembly / negative regulation of bacterial-type flagellum-dependent cell motility / positive regulation of single-species biofilm formation on inanimate substrate / diguanylate cyclase / diguanylate cyclase activity / cell pole / cell adhesion involved in single-species biofilm formation / metabolic process / GTP binding / protein homodimerization activity ...negative regulation of bacterial-type flagellum assembly / negative regulation of bacterial-type flagellum-dependent cell motility / positive regulation of single-species biofilm formation on inanimate substrate / diguanylate cyclase / diguanylate cyclase activity / cell pole / cell adhesion involved in single-species biofilm formation / metabolic process / GTP binding / protein homodimerization activity / zinc ion binding / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Zaehringer, F. / Schirmer, T. | ||||||
Citation | Journal: Structure / Year: 2013 Title: Structure and signaling mechanism of a zinc-sensory diguanylate cyclase. Authors: Zahringer, F. / Lacanna, E. / Jenal, U. / Schirmer, T. / Boehm, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tvk.cif.gz | 58.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tvk.ent.gz | 39.8 KB | Display | PDB format |
PDBx/mmJSON format | 3tvk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tv/3tvk ftp://data.pdbj.org/pub/pdb/validation_reports/tv/3tvk | HTTPS FTP |
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-Related structure data
Related structure data | 3t9oC 4h54C 1w25S C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 20492.170 Da / Num. of mol.: 1 / Fragment: unp residues 127-296 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b1535, JW1528, ydeG, ydeH / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P31129, diguanylate cyclase | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-TAR / | #5: Water | ChemComp-HOH / | Nonpolymer details | AUTHORS STATE THAT ONLY HALF OF RESIDUE C2E A 501 HAS BEEN MODELED. THE OTHER HALF OF THE 2-FOLD ...AUTHORS STATE THAT ONLY HALF OF RESIDUE C2E A 501 HAS BEEN MODELED. THE OTHER HALF OF THE 2-FOLD SYMMETRIC C2E LIGAND IS GENERATED BY A CRYSTALLOG | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.5 % |
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Crystal grow | Temperature: 293 K / pH: 8.5 Details: 100mM Tris, 22.5% PEG 4000, pH 8.5, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.979 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 21, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→51.21 Å / Num. obs: 17292 / % possible obs: 100 % / Redundancy: 12.5 % / Biso Wilson estimate: 19.75 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 24.1 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 12 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 7.6 / Rsym value: 0.346 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1W25 Resolution: 1.8→15 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0 / SU B: 2.22 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.117 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.5 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.85 Å / Total num. of bins used: 20
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