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- PDB-4bet: 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: 4bet | ||||||
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Title | Crystal structure of the Legionella pneumophila FIC domain-containing effector AnkX protein (inactive H229A mutant) in complex with cytidine-diphosphate-choline | ||||||
![]() | PHOSPHOCHOLINE TRANSFERASE ANKX | ||||||
![]() | TRANSFERASE / PHOSPHOCHOLINATION / TYPE IV SECRETION SYSTEM EFFECTOR / CYTIDINE- DIPHOSPHATE-CHOLINE | ||||||
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 | ![]() | 399.2 KB | Display | ![]() |
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PDB format | ![]() | 331.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 36.3 KB | Display | |
Data in CIF | ![]() | 50 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4bepSC ![]() 4berC ![]() 4besC 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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.470724, 0.003868, 0.882272), Vector: |
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Components
#1: Protein | Mass: 58284.461 Da / Num. of mol.: 2 / Fragment: FIC AND ANKYRIN REPEATS DOMAINS, RESIDUES 2-484 / Mutation: YES Source method: isolated from a genetically manipulated source Details: INACTIVE MUTANT / Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q5ZXN6, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.9 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.2 M LITHIUM SULFATE, 14% PEG 4000, 0.1 M TRIS PH 7.5 |
-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: 2.55→43.89 Å / Num. obs: 36935 / % possible obs: 98.7 % / Redundancy: 4.7 % / Biso Wilson estimate: 60.66 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.02 |
Reflection shell | Resolution: 2.55→2.7 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 1.75 / % possible all: 97.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4BEP Resolution: 2.55→43.89 Å / Cor.coef. Fo:Fc: 0.9232 / Cor.coef. Fo:Fc free: 0.8891 / SU R Cruickshank DPI: 0.637 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.545 / SU Rfree Blow DPI: 0.281 / SU Rfree Cruickshank DPI: 0.291 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
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Displacement parameters | Biso mean: 69.76 Å2
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Refine analyze | Luzzati coordinate error obs: 0.4 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→43.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.62 Å / Total num. of bins used: 19
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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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