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Yorodumi- PDB-6e12: Crystal Structure of the Alr8543 protein in complex with Oleic Ac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6000000000000 | |||||||||
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Title | Crystal Structure of the Alr8543 protein in complex with Oleic Acid and magnesium ion from Nostoc sp. PCC 7120, Northeast Structural Genomics Consortium Target NsR141 | |||||||||
Components | Alr8543 protein | |||||||||
Keywords | LIPID BINDING PROTEIN / alpha-beta protein / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG | |||||||||
Function / homology | Ubiquinone biosynthesis protein Coq4 / Coenzyme Q (ubiquinone) biosynthesis protein Coq4 / ubiquinone biosynthetic process / OLEIC ACID / Alr8543 protein Function and homology information | |||||||||
Biological species | Nostoc sp. (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å | |||||||||
Authors | Forouhar, F. / Neely, H. / Seetharaman, J. / Xiao, R. / Ciccosanti, C. / Patel, D. / Belote, R.L. / Everett, J.K. / Nair, R. / Acton, T.B. ...Forouhar, F. / Neely, H. / Seetharaman, J. / Xiao, R. / Ciccosanti, C. / Patel, D. / Belote, R.L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: Crystal Structure of the Alr8543 protein in complex with Oleic Acid and magnesium ion from Nostoc sp. PCC 7120, Northeast Structural Genomics Consortium Target NsR141 Authors: Forouhar, F. / Neely, H. / Seetharaman, J. / Xiao, R. / Ciccosanti, C. / Patel, D. / Belote, R.L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J. ...Authors: Forouhar, F. / Neely, H. / Seetharaman, J. / Xiao, R. / Ciccosanti, C. / Patel, D. / Belote, R.L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6e12.cif.gz | 188.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e12.ent.gz | 157.4 KB | Display | PDB format |
PDBx/mmJSON format | 6e12.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/6e12 ftp://data.pdbj.org/pub/pdb/validation_reports/e1/6e12 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 26054.684 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria) Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / Gene: alr8543 / Cell (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YJY7 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / | #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: 5.2 Å3/Da / Density % sol: 76 % |
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Crystal grow | Temperature: 277 K / Method: microbatch / pH: 5 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Reservoir solution: 100mM Citric Acid (pH 5) and 1.6M (NH4)2SO4, microbatch under oil, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97885 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 14, 2009 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97885 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→37.536 Å / Num. obs: 39307 / % possible obs: 92.75 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 39.6 Å2 / Rmerge(I) obs: 0.056 / Χ2: 1 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 7913 / Χ2: 0.61 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.4→37.536 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.53
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→37.536 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 65.4527 Å / Origin y: 39.2986 Å / Origin z: 24.2245 Å
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Refinement TLS group | Selection details: all |