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- PDB-2xjh: Structure and Copper-binding Properties of Methanobactins from Me... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xjh | |||||||||
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Title | Structure and Copper-binding Properties of Methanobactins from Methylosinus trichosporium OB3b | |||||||||
![]() | METHANOBACTIN MB-OB3B | |||||||||
![]() | OXIDOREDUCTASE / METAL TRANSPORT / METHANOTROPHS / OXAZALONE | |||||||||
Function / homology | ![]() 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 | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | El-Ghazouani, A. / Basle, A. / Firbank, S.J. / Knapp, C.W. / Gray, J. / Graham, D.W. / Dennison, C. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 19.3 KB | Display | ![]() |
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PDB format | ![]() | 14.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 414.3 KB | Display | ![]() |
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Full document | ![]() | 414.3 KB | Display | |
Data in XML | ![]() | 3.5 KB | Display | |
Data in CIF | ![]() | 4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xjiC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein/peptide | ![]() ![]() References: UniProt: E3YBA4, METHANOBACTIN, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases, superoxide dismutase #2: Chemical | #3: Chemical | #4: 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: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.41 Å3/Da / Density % sol: 13 % Description: PREVIOUSLY SOLVED MODEL CCDC BIDLOQ WAS MANUALLY FITTED INTO DENSITY |
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Crystal grow | pH: 7.5 / Details: 4M SODIUM FORMATE, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 0.92→20.84 Å / Num. obs: 9025 / % possible obs: 95.7 % / Observed criterion σ(I): 2 / Redundancy: 11.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 25.1 |
Reflection shell | Resolution: 0.92→0.97 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 5.5 / % possible all: 78.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 0.92→20 Å / Num. parameters: 1623 / Num. restraintsaints: 1871 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 13 / Occupancy sum hydrogen: 92 / Occupancy sum non hydrogen: 165.46 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.92→20 Å
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Refine LS restraints |
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