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Yorodumi- PDB-3zcb: VbhT Fic protein from Bartonella schoenbuchensis in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zcb | ||||||
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Title | VbhT Fic protein from Bartonella schoenbuchensis in complex with VbhA antitoxin mutant E24G and ATP | ||||||
Components |
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Keywords | TRANSFERASE/ANTITOXIN / TRANSFERASE-ANTITOXIN COMPLEX / AMPYLATION / ADENYLYLATION / TOXIN-ANTITOXIN COMPLEX | ||||||
Function / homology | Function and homology information negative regulation of protein adenylylation / AMPylase activity / protein adenylyltransferase / protein adenylylation / regulation of cell division / magnesium ion binding / protein homodimerization activity / ATP binding Similarity search - Function | ||||||
Biological species | BARTONELLA SCHOENBUCHENSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å | ||||||
Authors | Goepfert, A. / Schirmer, T. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Conserved Inhibitory Mechanism and Competent ATP Binding Mode for Adenylyltransferases with Fic Fold. Authors: Goepfert, A. / Stanger, F.V. / Dehio, C. / Schirmer, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zcb.cif.gz | 116.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zcb.ent.gz | 89.1 KB | Display | PDB format |
PDBx/mmJSON format | 3zcb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zcb_validation.pdf.gz | 806.8 KB | Display | wwPDB validaton report |
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Full document | 3zcb_full_validation.pdf.gz | 807 KB | Display | |
Data in XML | 3zcb_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 3zcb_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zc/3zcb ftp://data.pdbj.org/pub/pdb/validation_reports/zc/3zcb | HTTPS FTP |
-Related structure data
Related structure data | 3zc7C 3zcnC 3zecC 3zlmC 3shgS 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 on special symmetry positions |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 23208.004 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-198 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BARTONELLA SCHOENBUCHENSIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): AI References: UniProt: E6Z0R3, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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#2: Protein | Mass: 7176.108 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) BARTONELLA SCHOENBUCHENSIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): AI / References: UniProt: E6Z0R4 |
-Non-polymers , 4 types, 137 molecules
#3: Chemical | ChemComp-ATP / |
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#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-GOL / |
#6: 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: 2.29 Å3/Da / Density % sol: 46.4 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 16% W/V PEG4000, 0.1M MES PH6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9794 |
Detector | Type: DECTRIS PILATUS-2M / Detector: PIXEL / Date: Jun 15, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→45.44 Å / Num. obs: 19937 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.39 |
Reflection shell | Resolution: 1.94→2.06 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.34 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3SHG Resolution: 1.94→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.918 / SU B: 7.985 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.168 / 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: 25.976 Å2
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Refinement step | Cycle: LAST / Resolution: 1.94→30 Å
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Refine LS restraints |
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