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Yorodumi- PDB-5cmt: Fic protein from Neisseria meningitidis (NmFic) mutant E156R Y183... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cmt | ||||||
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Title | Fic protein from Neisseria meningitidis (NmFic) mutant E156R Y183F in dimeric form | ||||||
Components | Adenosine monophosphate-protein transferase NmFic | ||||||
Keywords | TRANSFERASE / Fic protein / AMP-transferase / dimer | ||||||
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 serogroup B (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 0.99 Å | ||||||
Authors | Stanger, F.V. / Schirmer, T. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: Intrinsic regulation of FIC-domain AMP-transferases by oligomerization and automodification. Authors: Stanger, F.V. / Burmann, B.M. / Harms, A. / Aragao, H. / Mazur, A. / Sharpe, T. / Dehio, C. / Hiller, S. / Schirmer, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cmt.cif.gz | 106 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cmt.ent.gz | 81.2 KB | Display | PDB format |
PDBx/mmJSON format | 5cmt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/5cmt ftp://data.pdbj.org/pub/pdb/validation_reports/cm/5cmt | HTTPS FTP |
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-Related structure data
Related structure data | 5cglC 5cklSC S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 22135.230 Da / Num. of mol.: 1 / Fragment: UNP residues 21-191 / Mutation: E156R Y183F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria) Gene: NMB0255 / Plasmid: pRSFDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q7DDR9, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases | ||||
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#2: Chemical | #3: Chemical | #4: 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: 2.74 Å3/Da / Density % sol: 54.79 % |
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Crystal grow | Temperature: 277.15 K / Method: batch mode / pH: 7.8 / Details: 10 mM Tris pH 7.8, 100 mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.8 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 11, 2013 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 0.99→47.22 Å / Num. obs: 126436 / % possible obs: 96.8 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.017 / Net I/σ(I): 23.4 / Num. measured all: 805863 / Scaling rejects: 135 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CKL Resolution: 0.99→47.22 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.1479 / WRfactor Rwork: 0.1273 / FOM work R set: 0.9139 / SU B: 0.595 / SU ML: 0.014 / SU R Cruickshank DPI: 0.0186 / SU Rfree: 0.0199 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.019 / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 86.39 Å2 / Biso mean: 11.055 Å2 / Biso min: 4.19 Å2
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Refinement step | Cycle: final / Resolution: 0.99→47.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.99→1.016 Å / Total num. of bins used: 20
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