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Yorodumi- PDB-3zlm: Fic protein from Neisseria meningitidis mutant E186G in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zlm | ||||||
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Title | Fic protein from Neisseria meningitidis mutant E186G in complex with AMPPNP | ||||||
Components | ADENOSINE MONOPHOSPHATE-PROTEIN TRANSFERASE NMFIC | ||||||
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: 2 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 | 3zlm.cif.gz | 91.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zlm.ent.gz | 69.6 KB | Display | PDB format |
PDBx/mmJSON format | 3zlm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/3zlm ftp://data.pdbj.org/pub/pdb/validation_reports/zl/3zlm | HTTPS FTP |
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-Related structure data
Related structure data | 3zc7C 3zcbC 3zcnC 3zecC 2g03S 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: 22051.088 Da / Num. of mol.: 1 / Fragment: RESIDUES 11-191 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) NEISSERIA MENINGITIDIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): AI References: UniProt: Q7DDR9, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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#2: Chemical | ChemComp-ANP / |
#3: Chemical | ChemComp-MG / |
#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: 5.8 Å3/Da / Density % sol: 78.8 % / Description: NONE |
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Crystal grow | pH: 9 Details: 4M POTASSIUM FORMATE, 0.1M BIS-TRIS PROPANE PH 9.0, 2% W/V PEG MME 2000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS-2M-F / Detector: PIXEL / Date: May 11, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→49.32 Å / Num. obs: 34254 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 21.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 30.91 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 22.6 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 5.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2G03 Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 5.915 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.089 / 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: 45.197 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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