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- PDB-4ber: Crystal structure of the Legionella pneumophila FIC domain-contai... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ber | ||||||
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Title | Crystal structure of the Legionella pneumophila FIC domain-containing effector AnkX protein in complex with cytidine monophosphate | ||||||
![]() | PHOSPHOCHOLINE TRANSFERASE ANKX | ||||||
![]() | TRANSFERASE / TYPE IV SECRETION SYSTEM EFFECTOR | ||||||
Function / homology | ![]() phosphocholine transferase activity / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / regulation of GTPase activity / host cell cytoplasm / transcription cis-regulatory region binding / positive regulation of transcription by RNA polymerase II / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Campanacci, V. / Mukherjee, S. / Roy, C.R. / Cherfils, J. | ||||||
![]() | ![]() Title: Structure of the Legionella Effector Ankx Reveals the Mechanism of Phosphocholine Transfer by the Fic Domain. Authors: Campanacci, V. / Mukherjee, S. / Roy, C.R. / Cherfils, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 392.1 KB | Display | ![]() |
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PDB format | ![]() | 324.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 34.5 KB | Display | |
Data in CIF | ![]() | 47.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4bepSC ![]() 4besC ![]() 4betC 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 54889.660 Da / Num. of mol.: 2 / Fragment: FIC AND ANKYRIN REPEATS DOMAINS, RESIDUES 2-484 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q5ZXN6, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor #2: Chemical | #3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.7 % / Description: NONE |
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Crystal grow | pH: 8.5 / Details: 15% PEG 20000, 0.1 M TRIS PH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 2, 2012 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→46.28 Å / Num. obs: 42690 / % possible obs: 99.6 % / Redundancy: 7.3 % / Biso Wilson estimate: 62.69 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 16.16 |
Reflection shell | Resolution: 2.6→2.76 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.01 / Mean I/σ(I) obs: 2.3 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4BEP Resolution: 2.6→46.28 Å / Cor.coef. Fo:Fc: 0.9145 / Cor.coef. Fo:Fc free: 0.894 / SU R Cruickshank DPI: 0.434 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.424 / SU Rfree Blow DPI: 0.259 / SU Rfree Cruickshank DPI: 0.264 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
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Displacement parameters | Biso mean: 66.29 Å2
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Refine analyze | Luzzati coordinate error obs: 0.405 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→46.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.67 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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