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- PDB-5o9k: Crystal structure of Murine Histmaine-Releasing Factor (HRF/TCTP) -
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Open data
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Basic information
Entry | Database: PDB / ID: 5o9k | ||||||
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Title | Crystal structure of Murine Histmaine-Releasing Factor (HRF/TCTP) | ||||||
![]() | Translationally-controlled tumor protein | ||||||
![]() | IMMUNE SYSTEM / Immunoglobulin E / Allergy / Histamine Releasing Factor / TCTP / HRF / P23 / P21 / Fortilin | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dore, K.A. / Kashiwakura, J. / McDonnell, J.M. / Gould, H.J. / Kawakami, T. / Sutton, B.J. / Davies, A.M. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 126.9 KB | Display | ![]() |
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PDB format | ![]() | 99.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.7 KB | Display | ![]() |
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Full document | ![]() | 434.5 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 14.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5o9lC ![]() 5o9mC ![]() 1yz1S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 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.) ![]() ![]() Production host: ![]() References: UniProt: P63028 #2: Chemical | ChemComp-GOL / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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