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Yorodumi- PDB-4bep: Crystal structure of the Legionella pneumophila FIC domain-contai... -
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-Basic information
Entry | Database: PDB / ID: 4bep | ||||||
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Title | Crystal structure of the Legionella pneumophila FIC domain-containing effector AnkX protein (apo-form) | ||||||
Components | PHOSPHOCHOLINE TRANSFERASE ANKX | ||||||
Keywords | TRANSFERASE / PHOSPHOCHOLINATION / TYPE IV SECRETION SYSTEM EFFECTOR | ||||||
Function / homology | Function and homology information phosphocholine transferase activity / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / regulation of GTPase activity / host cell cytoplasm / extracellular region Similarity search - Function | ||||||
Biological species | LEGIONELLA PNEUMOPHILA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.14 Å | ||||||
Authors | Campanacci, V. / Mukherjee, S. / Roy, C.R. / Cherfils, J. | ||||||
Citation | Journal: Embo J. / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bep.cif.gz | 388.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bep.ent.gz | 333.4 KB | Display | PDB format |
PDBx/mmJSON format | 4bep.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/4bep ftp://data.pdbj.org/pub/pdb/validation_reports/be/4bep | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (-0.214, 0.9482, -0.2348), Vector: |
-Components
#1: Protein | Mass: 58914.266 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.) LEGIONELLA PNEUMOPHILA (bacteria) / Strain: PHILADELPHIA 1 / Plasmid: PDEST17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS References: UniProt: Q5ZXN6, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor #2: Chemical | #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | Sequence details | L247P (CLONING ARTEFACT) N-TERMINAL HIS-6 TAG NOT CLEAVED BY TEV PROTEASE | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.7 % / Description: NONE |
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Crystal grow | pH: 8 Details: 0.2 M POTASSIUM THIOCYANATE, 15-25% PEG 3350, 0.05 M HEPES PH 7.8-8.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9792 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 8, 2010 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3.14→44 Å / Num. obs: 20682 / % possible obs: 98.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.33 |
Reflection shell | Resolution: 3.14→3.33 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.59 / % possible all: 96.9 |
-Processing
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Refinement | Method to determine structure: SAD / Resolution: 3.14→44 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.879 / SU B: 53.847 / SU ML: 0.425 / Cross valid method: THROUGHOUT / ESU R Free: 0.553 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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 mean: 108.032 Å2
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Refinement step | Cycle: LAST / Resolution: 3.14→44 Å
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Refine LS restraints |
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