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Yorodumi- PDB-3w9k: Crystal structure of thermoacidophile-specific protein STK_08120 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3w9k | ||||||
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Title | Crystal structure of thermoacidophile-specific protein STK_08120 complexed with myristic acid | ||||||
Components | FATTY ACID-BINDING PROTEIN | ||||||
Keywords | LIPID BINDING PROTEIN / Helix-Grip Fold / Fatty Acid Binding | ||||||
Function / homology | Protein of unknown function DUF3211 / STK_08120-like / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta / MYRISTIC ACID / DUF3211 domain-containing protein Function and homology information | ||||||
Biological species | Sulfolobus tokodaii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Miyakawa, T. / Sawano, Y. / Miyazono, K. / Miyauchi, Y. / Hatano, K. / Tanokura, M. | ||||||
Citation | Journal: J.Bacteriol. / Year: 2013 Title: A thermoacidophile-specific protein family, DUF3211, functions as a fatty acid carrier with novel binding mode. Authors: Miyakawa, T. / Sawano, Y. / Miyazono, K. / Miyauchi, Y. / Hatano, K. / Tanokura, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w9k.cif.gz | 43.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w9k.ent.gz | 29.2 KB | Display | PDB format |
PDBx/mmJSON format | 3w9k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3w9k_validation.pdf.gz | 432.2 KB | Display | wwPDB validaton report |
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Full document | 3w9k_full_validation.pdf.gz | 433 KB | Display | |
Data in XML | 3w9k_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 3w9k_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w9/3w9k ftp://data.pdbj.org/pub/pdb/validation_reports/w9/3w9k | HTTPS FTP |
-Related structure data
Related structure data | 2ejxSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16015.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: 7 / Gene: STK_08120 / Production host: Escherichia coli (E. coli) / References: UniProt: Q973T5 |
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#2: Chemical | ChemComp-MYR / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 23% (v/v) isopropanol, 0.2M ammonium acetate, 0.1M Tris-HCl, pH 8.0 , VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 30, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 13006 / Observed criterion σ(I): 45.4 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 8.5 / Rsym value: 0.214 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2EJX Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.566 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.134 / 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: 18.58 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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