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Yorodumi- PDB-3se5: Fic protein from NEISSERIA MENINGITIDIS mutant delta8 in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3se5 | ||||||
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Title | Fic protein from NEISSERIA MENINGITIDIS mutant delta8 in complex with AMPPNP | ||||||
Components | Cell filamentation protein Fic-related protein | ||||||
Keywords | TRANSFERASE / AMPylation / adenylylation | ||||||
Function / homology | Function and homology information AMPylase activity / protein adenylyltransferase / protein adenylylation / regulation of cell division / protein homodimerization activity / ATP binding Similarity search - Function | ||||||
Biological species | Neisseria meningitidis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Goepfert, A. / Stanger, F. / Schirmer, T. | ||||||
Citation | Journal: Nature / Year: 2012 Title: Adenylylation control by intra- or intermolecular active-site obstruction in Fic proteins. Authors: Engel, P. / Goepfert, A. / Stanger, F.V. / Harms, A. / Schmidt, A. / Schirmer, T. / Dehio, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3se5.cif.gz | 152.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3se5.ent.gz | 119 KB | Display | PDB format |
PDBx/mmJSON format | 3se5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/se/3se5 ftp://data.pdbj.org/pub/pdb/validation_reports/se/3se5 | HTTPS FTP |
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-Related structure data
Related structure data | 3s6aC 3shgC 3sn9C 2g03S 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: 19222.021 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: serogroup B / Gene: NMB0255 / Plasmid: pRSFDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 AI / References: UniProt: Q7DDR9 #2: Chemical | ChemComp-ANP / #3: Chemical | ChemComp-P6G / #4: Chemical | ChemComp-MG / #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 | Density Matthews: 2.27 Å3/Da / Density % sol: 45.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 44% w/v PEG 600, 0.1M Na-citrate, pH 5.6, 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: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 14, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Number: 295536 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→37.03 Å / Num. obs: 73865 / % possible obs: 97.69 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 9.8144 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2g03 Resolution: 1.7→15 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0 / SU B: 1.713 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.098 / 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 max: 75.46 Å2 / Biso mean: 19.233 Å2 / Biso min: 6.07 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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