+Open data
-Basic information
Entry | Database: PDB / ID: 3wur | ||||||
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Title | Structure of DMP19 Complex with 18-crown-6 | ||||||
Components | Uncharacterized protein | ||||||
Keywords | GENE REGULATION / helix bundle / DNA mimic | ||||||
Function / homology | A middle domain of Talin 1 - #60 / Domain of unknown function DUF4375 / Domain of unknown function (DUF4375) / A middle domain of Talin 1 / Up-down Bundle / Mainly Alpha / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE / L(+)-TARTARIC ACID / DUF4375 domain-containing protein Function and homology information | ||||||
Biological species | Neisseria meningitidis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å | ||||||
Authors | Lee, C.C. / Wang, H.C. / Wang, A.H.J. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2014 Title: Crowning proteins: modulating the protein surface properties using crown ethers. Authors: Lee, C.C. / Maestre-Reyna, M. / Hsu, K.C. / Wang, H.C. / Liu, C.I. / Jeng, W.Y. / Lin, L.L. / Wood, R. / Chou, C.C. / Yang, J.M. / Wang, A.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wur.cif.gz | 93.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wur.ent.gz | 70.9 KB | Display | PDB format |
PDBx/mmJSON format | 3wur.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wu/3wur ftp://data.pdbj.org/pub/pdb/validation_reports/wu/3wur | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 19357.438 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: MC58 / Gene: NMB0541 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9K0P4 |
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-Non-polymers , 5 types, 499 molecules
#2: Chemical | ChemComp-O4B / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-TLA / | #6: 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: 2.57 Å3/Da / Density % sol: 52.17 % |
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Crystal grow | Temperature: 298 K / pH: 5.6 Details: 0.2M Potassium sodium tartrate, 0.1M Na citrate, 1.6M Ammonium sulfate , pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 10, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→30 Å / Num. obs: 71243 / % possible obs: 98 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.041 / Rsym value: 0.041 / Net I/σ(I): 58.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.45→29.6 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / SU B: 0.894 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.09 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→29.6 Å
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Refine LS restraints |
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