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Yorodumi- PDB-4eyy: Crystal Structure of the IcmR-IcmQ complex from Legionella pneumophila -
+Open data
-Basic information
Entry | Database: PDB / ID: 4eyy | ||||||
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Title | Crystal Structure of the IcmR-IcmQ complex from Legionella pneumophila | ||||||
Components |
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Keywords | PROTEIN BINDING / Protein heterodimer / ADPRT-like fold / NAD-binding domain | ||||||
Function / homology | Function and homology information Dot/Icm secretion system IcmQ, C-terminal domain / : / IcmR, middle region / ADP-ribosylation fold / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Alpha-Beta Barrel / Up-down Bundle / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Legionella pneumophila subsp. pneumophila (bacteria) Legionella pneumophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å | ||||||
Authors | Farelli, J.D. / Gumbart, J. / Akey, I.V. / Amyot, W. / Hempstead, A.D. / Head, J.F. / McKnight, C.J. / Isberg, R.R. / Akey, C.W. | ||||||
Citation | Journal: Structure / Year: 2013 Title: IcmQ in the Type 4b secretion system contains an NAD+ binding domain. Authors: Farelli, J.D. / Gumbart, J.C. / Akey, I.V. / Hempstead, A. / Amyot, W. / Head, J.F. / McKnight, C.J. / Isberg, R.R. / Akey, C.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4eyy.cif.gz | 65.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4eyy.ent.gz | 48.5 KB | Display | PDB format |
PDBx/mmJSON format | 4eyy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/4eyy ftp://data.pdbj.org/pub/pdb/validation_reports/ey/4eyy | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-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: 12961.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria) Strain: Philadelphia 1 / Gene: icmR, lpg0443 / Plasmid: pQE70 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 (REP4) / References: UniProt: Q5ZYC9 |
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#2: Protein | Mass: 21514.600 Da / Num. of mol.: 1 / Mutation: K57Q, K59Q, R67Q, R71Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila (bacteria) / Strain: Corby / Gene: icmQ, LPC_2899 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 (REP4) / References: UniProt: A5IHF0 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal |
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Crystal grow | Temperature: 294 K Details: Protein concentration 8 mg/ml. Selenomethionine-incorporated protein for SAD phasing. 1:1 ratio of protein to 24% PEG 1500, 0.1 M sodium citrate pH 5.9, 1 mM DTT and 1% ethylene glycol. ...Details: Protein concentration 8 mg/ml. Selenomethionine-incorporated protein for SAD phasing. 1:1 ratio of protein to 24% PEG 1500, 0.1 M sodium citrate pH 5.9, 1 mM DTT and 1% ethylene glycol. Cryoprotected in mother liquor + 30% ethylene glycol and frozen in liquid nitrogen, VAPOR DIFFUSION, HANGING DROP, temperature 294K PH range: 5.9; 7.5 |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.4→19.754 Å / Num. obs: 15596 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Biso Wilson estimate: 45.63 Å2 / Rmerge(I) obs: 0.208 / Rsym value: 0.054 / Net I/σ(I): 20.8 | ||||||||||||||||||
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 5.4 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.4→19.75 Å / SU ML: 0.37 / σ(F): 1.35 / Phase error: 28.01 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.51 Å2 / ksol: 0.17 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.4→19.75 Å
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Refine LS restraints |
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LS refinement shell |
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