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Yorodumi- PDB-3kb1: Crystal Structure of the Nucleotide-binding protein AF_226 in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kb1 | ||||||
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Title | Crystal Structure of the Nucleotide-binding protein AF_226 in complex with ADP from Archaeoglobus fulgidus, Northeast Structural Genomics Consortium Target GR157 | ||||||
Components | Nucleotide-binding protein | ||||||
Keywords | Nucleotide binding protein / alpha-beta protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
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: 2.9 Å | ||||||
Authors | Forouhar, F. / Lew, S. / Abashidze, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. ...Forouhar, F. / Lew, S. / Abashidze, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Northeast Structural Genomics Consortium Target GR157 Authors: Forouhar, F. / Lew, S. / Abashidze, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kb1.cif.gz | 105.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kb1.ent.gz | 85.3 KB | Display | PDB format |
PDBx/mmJSON format | 3kb1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/3kb1 ftp://data.pdbj.org/pub/pdb/validation_reports/kb/3kb1 | 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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Unit cell |
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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) / Strain: DSM 4304 / Gene: AF_2269 / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: O28015 #2: Chemical | #3: Chemical | ChemComp-ZN / | #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 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 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 |
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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 / Protocol: SINGLE WAVELENGTH / 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. all: 26841 / Num. obs: 26385 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 41.5 Å2 / 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 / Mean I/σ(I) obs: 3.07 / Rsym value: 0.22 / % possible all: 88.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.9→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 471928.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 32.1139 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 10
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