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Yorodumi- PDB-2yz2: Crystal structure of the ABC transporter in the cobalt transport ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yz2 | ||||||
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Title | Crystal structure of the ABC transporter in the cobalt transport system | ||||||
Components | Putative ABC transporter ATP-binding protein TM_0222 | ||||||
Keywords | HYDROLASE / ABC Transporter / Cobalt transport / ATP-binding protein / TM0222 / Inner membrane / Membrane / Nucleotide-binding / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information Translocases / riboflavin transport / riboflavin transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Ethayathullah, A.S. / Bessho, Y. / Padmanabhan, B. / Singh, T.P. / Kaur, P. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the ABC transporter in the cobalt transport system Authors: Ethayathullah, A.S. / Bessho, Y. / Padmanabhan, B. / Singh, T.P. / Kaur, P. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yz2.cif.gz | 123.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yz2.ent.gz | 98.6 KB | Display | PDB format |
PDBx/mmJSON format | 2yz2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/2yz2 ftp://data.pdbj.org/pub/pdb/validation_reports/yz/2yz2 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30276.000 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL-X References: UniProt: Q9WY65, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances #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: 2.81 Å3/Da / Density % sol: 56.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2M potassium flouride, 20% (w/v) PEG 3350 (PEG/ION-2), pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 120 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97891, 0.90000, 0.97934 | ||||||||||||
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD | ||||||||||||
Radiation | Monochromator: Si double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.3→50 Å / Num. all: 31565 / Num. obs: 31555 / % possible obs: 100 % / Observed criterion σ(F): -3 / Redundancy: 21.3 % / Rmerge(I) obs: 0.117 | ||||||||||||
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 17.8 % / Rmerge(I) obs: 0.49 / Num. unique all: 3095 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.83 / SU B: 7.397 / SU ML: 0.189 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.38 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 mean: 42.895 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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