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- PDB-3zlm: Fic protein from Neisseria meningitidis mutant E186G in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3zlm | ||||||
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Title | Fic protein from Neisseria meningitidis mutant E186G in complex with AMPPNP | ||||||
![]() | ADENOSINE MONOPHOSPHATE-PROTEIN TRANSFERASE NMFIC | ||||||
![]() | TRANSFERASE / AMPYLATION / ADENYLYLATION | ||||||
Function / homology | ![]() AMPylase activity / protein adenylyltransferase / protein adenylylation / regulation of cell division / protein homodimerization activity / ATP binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Goepfert, A. / Schirmer, T. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 91.7 KB | Display | ![]() |
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PDB format | ![]() | 69.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 802 KB | Display | ![]() |
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Full document | ![]() | 802.1 KB | Display | |
Data in XML | ![]() | 10.4 KB | Display | |
Data in CIF | ![]() | 14.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3zc7C ![]() 3zcbC ![]() 3zcnC ![]() 3zecC ![]() 2g03S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() 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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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