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Yorodumi- PDB-5o9k: Crystal structure of Murine Histmaine-Releasing Factor (HRF/TCTP) -
+Open data
-Basic information
Entry | Database: PDB / ID: 5o9k | ||||||
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Title | Crystal structure of Murine Histmaine-Releasing Factor (HRF/TCTP) | ||||||
Components | Translationally-controlled tumor protein | ||||||
Keywords | IMMUNE SYSTEM / Immunoglobulin E / Allergy / Histamine Releasing Factor / TCTP / HRF / P23 / P21 / Fortilin | ||||||
Function / homology | Function and homology information negative regulation of ectoderm development / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / stem cell population maintenance / cytoplasmic microtubule / transcription factor binding / multivesicular body / spindle pole / spermatogenesis / calcium ion binding / extracellular space ...negative regulation of ectoderm development / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / stem cell population maintenance / cytoplasmic microtubule / transcription factor binding / multivesicular body / spindle pole / spermatogenesis / calcium ion binding / extracellular space / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.014 Å | ||||||
Authors | Dore, K.A. / Kashiwakura, J. / McDonnell, J.M. / Gould, H.J. / Kawakami, T. / Sutton, B.J. / Davies, A.M. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Mol. Immunol. / Year: 2017 Title: Crystal structures of murine and human Histamine-Releasing Factor (HRF/TCTP) and a model for HRF dimerisation in mast cell activation. Authors: Dore, K.A. / Kashiwakura, J.I. / McDonnell, J.M. / Gould, H.J. / Kawakami, T. / Sutton, B.J. / Davies, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o9k.cif.gz | 126.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o9k.ent.gz | 99.4 KB | Display | PDB format |
PDBx/mmJSON format | 5o9k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5o9k_validation.pdf.gz | 433.7 KB | Display | wwPDB validaton report |
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Full document | 5o9k_full_validation.pdf.gz | 434.5 KB | Display | |
Data in XML | 5o9k_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 5o9k_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o9/5o9k ftp://data.pdbj.org/pub/pdb/validation_reports/o9/5o9k | HTTPS FTP |
-Related structure data
Related structure data | 5o9lC 5o9mC 1yz1S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20556.314 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Murine histamine-releasing factor with C-terminal His-tag Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tpt1, Trt Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) References: UniProt: P63028 #2: Chemical | ChemComp-GOL / | |
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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: 2.43 Å3/Da / Density % sol: 49.3 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.4 Details: 0.1M Tris-HCl pH8.4, 23% (w/v) PEG 2000 MME and 0.01M nickel chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 A |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 28, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 4.01→57.06 Å / Num. obs: 3606 / % possible obs: 98.5 % / Redundancy: 11.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.271 / Rpim(I) all: 0.081 / Net I/σ(I): 9 |
Reflection shell | Resolution: 4.01→4.63 Å / Redundancy: 12 % / Rmerge(I) obs: 1.892 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1200 / CC1/2: 0.877 / Rpim(I) all: 0.554 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YZ1 Resolution: 4.014→57.059 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 28.19
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.014→57.059 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.0142→57.0647 Å
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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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