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Yorodumi- PDB-3t66: Crystal structure of Nickel ABC transporter from Bacillus halodurans -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t66 | ||||||
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Title | Crystal structure of Nickel ABC transporter from Bacillus halodurans | ||||||
Components | Nickel ABC transporter (Nickel-binding protein) | ||||||
Keywords | TRANSPORT PROTEIN / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / periplasmic protein / Nickel ABC transporter | ||||||
Function / homology | Function and homology information ATP-binding cassette (ABC) transporter complex / transmembrane transport / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus halodurans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Agarwal, R. / Bonanno, J.B. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. ...Agarwal, R. / Bonanno, J.B. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of Nickel ABC transporter from Bacillus halodurans Authors: Agarwal, R. / Bonanno, J.B. / Almo, S.C. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t66.cif.gz | 101.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t66.ent.gz | 75.3 KB | Display | PDB format |
PDBx/mmJSON format | 3t66.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3t66_validation.pdf.gz | 431.6 KB | Display | wwPDB validaton report |
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Full document | 3t66_full_validation.pdf.gz | 439.4 KB | Display | |
Data in XML | 3t66_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | 3t66_validation.cif.gz | 25.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t6/3t66 ftp://data.pdbj.org/pub/pdb/validation_reports/t6/3t66 | HTTPS FTP |
-Related structure data
Related structure data | 3rqtS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 55743.324 Da / Num. of mol.: 1 / Fragment: Nickel ABC transporter / Mutation: Native Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus halodurans (bacteria) / Strain: C-125 / Gene: BH1796 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL / References: UniProt: Q9KBX8 |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.96 % |
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Crystal grow | Temperature: 298 K / pH: 7.5 Details: 0.2M CaCl2,0.1M HEPES, 28%PEG 400, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.08 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 21, 2011 / Details: MIRRORS |
Radiation | Monochromator: SI-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 16232 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 19.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 19.6 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 5 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3RQT Resolution: 2.8→19.98 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.9 / SU B: 14.638 / SU ML: 0.284 / Cross valid method: THROUGHOUT / ESU R: 0.778 / ESU R Free: 0.363 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→19.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.87 Å / Total num. of bins used: 20
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