+Open data
-Basic information
Entry | Database: PDB / ID: 4kku | ||||||
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Title | Structure of BesA (Selenomethinone derivative - P212121) | ||||||
Components | Membrane fusion protein | ||||||
Keywords | MEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Borrelia burgdorferi (Lyme disease spirochete) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å | ||||||
Authors | Greene, N.P. / Hinchliffe, P. / Crow, A. / Ababou, A. / Hughes, C. / Koronakis, V. | ||||||
Citation | Journal: Febs Lett. / Year: 2013 Title: Structure of an atypical periplasmic adaptor from a multidrug efflux pump of the spirochete Borrelia burgdorferi. Authors: Greene, N.P. / Hinchliffe, P. / Crow, A. / Ababou, A. / Hughes, C. / Koronakis, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kku.cif.gz | 214.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kku.ent.gz | 179.4 KB | Display | PDB format |
PDBx/mmJSON format | 4kku.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kk/4kku ftp://data.pdbj.org/pub/pdb/validation_reports/kk/4kku | 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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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Details | THE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN. |
-Components
#1: Protein | Mass: 32745.141 Da / Num. of mol.: 4 / Fragment: UNP residues 26-317 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete) Strain: ATCC 35210 / B31 / CIP 102532 / DSM 4680 / Gene: BB_0141 / Production host: Escherichia coli (E. coli) / References: UniProt: O51166 #2: 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: 3.33 Å3/Da / Density % sol: 63.06 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 100 mM phosphate/citrate pH 4.2, 100 mM LiSO4, 16 % (w/v) PEG 1000, VAPOR DIFFUSION, SITTING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9787 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2012 |
Radiation | Monochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→77.74 Å / Num. all: 72616 / Num. obs: 72616 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.35→2.4 Å / % possible all: 88.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.35→77.74 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.832 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.278 / ESU R Free: 0.222 / 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: 42.892 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→77.74 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.35→2.411 Å / Total num. of bins used: 20
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