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Yorodumi- PDB-3wea: Crystal structure of a Niemann-Pick type C2 protein from Japanese... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wea | ||||||
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Title | Crystal structure of a Niemann-Pick type C2 protein from Japanese carpenter ant | ||||||
Components | Niemann-Pick type C2 protein | ||||||
Keywords | LIPID BINDING PROTEIN / immunoglobulin-like beta-sandwich fold / carrier protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Camponotus japonicus (insect) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Fujimoto, Z. / Tsuchiya, W. / Ishida, Y. / Yamazaki, T. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Niemann-Pick type C2 protein mediating chemical communication in the worker ant Authors: Ishida, Y. / Tsuchiya, W. / Fujii, T. / Fujimoto, Z. / Miyazawa, M. / Ishibashi, J. / Matsuyama, S. / Ishikawa, Y. / Yamazaki, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wea.cif.gz | 65.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wea.ent.gz | 48.8 KB | Display | PDB format |
PDBx/mmJSON format | 3wea.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wea_validation.pdf.gz | 431.2 KB | Display | wwPDB validaton report |
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Full document | 3wea_full_validation.pdf.gz | 434.3 KB | Display | |
Data in XML | 3wea_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 3wea_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/we/3wea ftp://data.pdbj.org/pub/pdb/validation_reports/we/3wea | HTTPS FTP |
-Related structure data
Related structure data | 3webC 2hkaS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 14927.394 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Camponotus japonicus (insect) / Gene: CjapNPC2 / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: W5JXD9*PLUS #2: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEB | |
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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: 2.53 Å3/Da / Density % sol: 51.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 25% (w/v) PEG 3350, 0.2mM sodium chloride, 0.1M HEPES buffer, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 4, 2010 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→104.843 Å / Num. obs: 28166 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 22.229 Å2 / Rsym value: 0.101 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 3 / Num. unique all: 2747 / Rsym value: 0.495 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2HKA Resolution: 1.8→22.42 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.876 / SU B: 4.772 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 38.333 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→22.42 Å
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Refine LS restraints |
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