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Yorodumi- PDB-2vox: An oxidized tryptophan facilitates copper-binding in Methylococcu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vox | ||||||
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Title | An oxidized tryptophan facilitates copper-binding in Methylococcus capsulatus secreted protein MopE. The structure of mercury soaked MopE to 1.9AA | ||||||
Components | SURFACE-ASSOCIATED PROTEIN | ||||||
Keywords | METAL BINDING PROTEIN / METAL-BINDING PROTEIN / OXIDIZED TRYPTOPHAN / METHANOTROPH BACTERIUM / KUNURENINE / COPPER HOMEOSTASIS | ||||||
Function / homology | Function and homology information | ||||||
Biological species | METHYLOCOCCUS CAPSULATUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | ||||||
Authors | Helland, R. / Fjellbirkeland, A. / Karlsen, O.A. / Ve, T. / Lillehaug, J.R. / Jensen, H.B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: An Oxidized Tryptophan Facilitates Copper Binding in Methylococcus Capsulatus-Secreted Protein Mope. Authors: Helland, R. / Fjellbirkeland, A. / Karlsen, O.A. / Ve, T. / Lillehaug, J.R. / Jensen, H.B. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vox.cif.gz | 66.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vox.ent.gz | 53.2 KB | Display | PDB format |
PDBx/mmJSON format | 2vox.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vox_validation.pdf.gz | 428 KB | Display | wwPDB validaton report |
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Full document | 2vox_full_validation.pdf.gz | 430.1 KB | Display | |
Data in XML | 2vox_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 2vox_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vo/2vox ftp://data.pdbj.org/pub/pdb/validation_reports/vo/2vox | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36185.836 Da / Num. of mol.: 1 / Fragment: RESIDUES 205-540 / Source method: isolated from a natural source / Details: UNIVERSITY OF WARWICK CULTURE COLLECTION / Source: (natural) METHYLOCOCCUS CAPSULATUS (bacteria) / Strain: BATH, NCIMB 11132 / References: UniProt: Q9AIP9, UniProt: G1UBC6*PLUS | ||
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#2: Chemical | ChemComp-CA / | ||
#3: Chemical | ChemComp-CU / | ||
#4: Chemical | ChemComp-HG / | ||
#5: Water | ChemComp-HOH / | ||
Nonpolymer details | KYNURENINESequence details | THE PURIFIED MOPE REPRESENTS THE 336 C-TERMINAL RESIDUES OF THE SEQUENCE. THE 46 N-TERMINAL ...THE PURIFIED MOPE REPRESENTS | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.61 % / Description: NONE |
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Crystal grow | pH: 7 Details: 36-45% AMMONIUM SULPHATE, 0.1 M BISTRIS PH 7.0-7.75 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.0085 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0085 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→41.1 Å / Num. obs: 27480 / % possible obs: 98.2 % / Redundancy: 13.4 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.3 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.9→41.13 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.099 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TRYPTOPHAN 130 IS POST-TRANSLATIONALLY OXIDIZED TO KYNURENINE RESIDUES 1-46 WERE NOT OBSERVED IN ELECTRON DENSITY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.01 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→41.13 Å
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Refine LS restraints |
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