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Yorodumi- PDB-2xji: Structure and Copper-binding Properties of Methanobactins from Me... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xji | |||||||||
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Title | Structure and Copper-binding Properties of Methanobactins from Methylosinus trichosporium OB3b | |||||||||
Components | METHANOBACTIN MB-OB3B | |||||||||
Keywords | OXIDOREDUCTASE / METAL TRANSPORT / METHANOTROPHS / OXAZALONE | |||||||||
Function / homology | Function and homology information copper ion transport / superoxide dismutase / superoxide dismutase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity / extracellular region / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | METHYLOSINUS TRICHOSPORIUM (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1 Å | |||||||||
Authors | El-Ghazouani, A. / Basle, A. / Firbank, S.J. / Knapp, C.W. / Gray, J. / Graham, D.W. / Dennison, C. | |||||||||
Citation | Journal: Inorg.Chem. / Year: 2011 Title: Copper-Binding Properties and Structures of Methanobactins from Methylosinus Trichosporium Ob3B. Authors: El Ghazouani, A. / Basle, A. / Firbank, S.J. / Knapp, C.W. / Gray, J. / Graham, D.W. / Dennison, C. #1: Journal: Science / Year: 2004 Title: Methanobactin, a Copper-Acquisition Compound from Methane-Oxidizing Bacteria. Authors: Kim, H.J. / Graham, D.W. / Dispirito, A.A. / Alterman, M.A. / Galeva, N. / Larive, C.K. / Asunskis, D. / Sherwood, P.M.A. #2: Journal: J.Am.Chem.Soc. / Year: 2008 Title: NMR, Mass Spectrometry and Chemical Evidence Reveal a Different Chemical Structure for Methanobactin that Contains Oxazolone Rings. Authors: Behling, L.A. / Hartsel, S.C. / Lewis, D.E. / Dispirito, A.A. / Choi, D.W. / Masterson, L.R. / Veglia, G. / Gallagher, W.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xji.cif.gz | 41.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xji.ent.gz | 34.2 KB | Display | PDB format |
PDBx/mmJSON format | 2xji.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xj/2xji ftp://data.pdbj.org/pub/pdb/validation_reports/xj/2xji | HTTPS FTP |
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-Related structure data
Related structure data | 2xjhC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein/peptide | Type: Chalkophore, Polypeptide / Class: Metal transport / Mass: 1161.373 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: NCIMB 11131 / Source: (natural) METHYLOSINUS TRICHOSPORIUM (bacteria) / Strain: OB3B References: UniProt: E3YBA4, METHANOBACTIN, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases, superoxide dismutase #2: Chemical | ChemComp-CU / #3: Water | ChemComp-HOH / | Compound details | METHANOBACTIN IS A MEMBER OF THE FAMILY OF CHALKOPHORES, A COPPER CHELATING AGENT INVOLVED IN ...METHANOBAC | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.15 % Description: PREVIOUSLY SOLVED MODEL CCDC BIDLOQ WAS MANUALLY FITTED INTO DENSITY |
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Crystal grow | pH: 7.5 / Details: 2M AMMONIUM SULFATE, 5% ISOPROPANOL, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.91 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 1, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 1→21.14 Å / Num. obs: 29329 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1→1.05 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 13.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1→20 Å / Num. parameters: 5724 / Num. restraintsaints: 8640 / Cross valid method: FREE R-VALUE / σ(F): 2 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 35 / Occupancy sum hydrogen: 252 / Occupancy sum non hydrogen: 471 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→20 Å
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Refine LS restraints |
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