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Yorodumi- PDB-4ber: Crystal structure of the Legionella pneumophila FIC domain-contai... -
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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 | ||||||
Components | PHOSPHOCHOLINE TRANSFERASE ANKX | ||||||
Keywords | TRANSFERASE / 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 / transcription cis-regulatory region binding / host cell cytoplasm / positive regulation of transcription by RNA polymerase II / extracellular region Similarity search - Function | ||||||
Biological species | LEGIONELLA PNEUMOPHILA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 | 4ber.cif.gz | 392.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ber.ent.gz | 324.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ber.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ber_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4ber_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4ber_validation.xml.gz | 34.5 KB | Display | |
Data in CIF | 4ber_validation.cif.gz | 47.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/4ber ftp://data.pdbj.org/pub/pdb/validation_reports/be/4ber | HTTPS FTP |
-Related structure data
Related structure data | 4bepSC 4besC 4betC 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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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.) LEGIONELLA PNEUMOPHILA (bacteria) / Strain: PHILADELPHIA 1 / 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-PO4 / #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
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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: 2.9 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: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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