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Yorodumi- PDB-6oby: The nucleotide-binding protein AF_226 in complex with ADP from Ar... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6oby | ||||||
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Title | The nucleotide-binding protein AF_226 in complex with ADP from Archaeoglobus fulgidus with Co found by PIXE. Based on 3KB1. | ||||||
Components | Iron-sulfur cluster carrier protein | ||||||
Keywords | METAL TRANSPORT / ALPHA-BETA PROTEIN / PIXE | ||||||
Function / homology | Function and homology information ATP-dependent FeS chaperone activity / iron-sulfur cluster assembly / iron-sulfur cluster binding / ATP hydrolysis activity / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.87 Å | ||||||
Authors | Snell, E.H. / Garman, E.F. / Lowe, E.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2020 Title: High-Throughput PIXE as an Essential Quantitative Assay for Accurate Metalloprotein Structural Analysis: Development and Application. Authors: Grime, G.W. / Zeldin, O.B. / Snell, M.E. / Lowe, E.D. / Hunt, J.F. / Montelione, G.T. / Tong, L. / Snell, E.H. / Garman, E.F. | ||||||
History |
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Remark 0 | THIS ENTRY 6OBY REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 3KB1, DETERMINED BY F. ...THIS ENTRY 6OBY REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 3KB1, DETERMINED BY F.FOROUHAR,S.LEW,M.ABASHIDZE,J.SEETHARAMAN,M.MAO,R.XIAO, C.CICCOSANTI,H.WANG,J.K.EVERETT,R.NAIR,T.B.ACTON,B.ROST,.T.MONTELIONE,J.F.HUNT,L.TONG,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6oby.cif.gz | 106.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6oby.ent.gz | 85.4 KB | Display | PDB format |
PDBx/mmJSON format | 6oby.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ob/6oby ftp://data.pdbj.org/pub/pdb/validation_reports/ob/6oby | 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:
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-Components
#1: Protein | Mass: 29462.975 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Plasmid: PET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)+ MAGIC / References: UniProt: O28015 #2: Chemical | #3: Chemical | ChemComp-CO / | #4: 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: 2.35 Å3/Da / Density % sol: 47.56 % / Description: Authors used the sf data from the entry 3KB1 |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PROTEIN SOLUTION: 100MM NACL, 5MM DTT, 0.02% NAN3, 10MM TRIS-HCL (PH 7.5). RESERVOIR SOLUTION: 100 MM NAACETATE (PH 4.6), 30% MPD, AND 200 MM NACL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97899 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 7, 2009 / Details: MIRRORS |
Radiation | Monochromator: SI 111 CHANNEL MIRRORS / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97899 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 26385 / % possible obs: 98.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.093 / Rsym value: 0.076 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.254 / Num. unique obs: 0 / Rsym value: 0.22 / % possible all: 88.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.87→28.54 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.859 / SU B: 23.812 / SU ML: 0.43 / Cross valid method: THROUGHOUT / ESU R Free: 0.481 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.987 Å2
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Refinement step | Cycle: LAST / Resolution: 2.87→28.54 Å
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Refine LS restraints |
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