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Yorodumi- PDB-4dve: Crystal structure at 2.1 A of the S-component for biotin from an ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dve | ||||||
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Title | Crystal structure at 2.1 A of the S-component for biotin from an ECF-type ABC transporter | ||||||
Components | Biotin transporter BioY | ||||||
Keywords | TRANSPORT PROTEIN / ECF-transport / Ligand-binding domain / biotin binding / Membrane | ||||||
Function / homology | Function and homology information biotin transmembrane transporter activity / membrane => GO:0016020 / plasma membrane Similarity search - Function | ||||||
Biological species | Lactococcus lactis subsp. cremoris (lactic acid bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.09 Å | ||||||
Authors | Berntsson, R.P.-A. / ter Beek, J. / Majsnerowska, M. / Duurkens, R. / Puri, P. / Poolman, B. / Slotboom, D.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Structural divergence of paralogous S components from ECF-type ABC transporters. Authors: Berntsson, R.P. / Ter Beek, J. / Majsnerowska, M. / Duurkens, R.H. / Puri, P. / Poolman, B. / Slotboom, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dve.cif.gz | 227 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dve.ent.gz | 191.1 KB | Display | PDB format |
PDBx/mmJSON format | 4dve.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/4dve ftp://data.pdbj.org/pub/pdb/validation_reports/dv/4dve | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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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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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 21952.320 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis subsp. cremoris (lactic acid bacteria) Strain: MG1363 / Gene: bioY, llmg_1964 / Production host: Lactococcus lactis (lactic acid bacteria) / Strain (production host): NZ9000 / References: UniProt: A2RMJ9 #2: Chemical | #3: Sugar | ChemComp-BNG / #4: 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: 3.27 Å3/Da / Density % sol: 62.4 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.05-0.2 mM CaCl2, 45-50% PEG400, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97935 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.09→48.36 Å / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 47.97 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 15.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.09→48.36 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.2049 / WRfactor Rwork: 0.1869 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9118 / SU B: 5.159 / SU ML: 0.068 / SU R Cruickshank DPI: 0.1592 / SU Rfree: 0.1357 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: WITH TLS ADDED
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.41 Å2 / Biso mean: 47.026 Å2 / Biso min: 25.76 Å2
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Refinement step | Cycle: LAST / Resolution: 2.09→48.36 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.094→2.148 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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