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- PDB-4tru: Crystal structure of Q24A Q25A mutant of human macrophage migrati... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4tru | ||||||
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Title | Crystal structure of Q24A Q25A mutant of human macrophage migration inhibitory factor | ||||||
![]() | Macrophage migration inhibitory factor![]() | ||||||
![]() | ![]() ![]() ![]() | ||||||
Function / homology | ![]() positive regulation of prostaglandin secretion involved in immune response / positive regulation of myeloid leukocyte cytokine production involved in immune response / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Pantouris, G. / Lolis, E. | ||||||
![]() | ![]() Title: An Analysis of MIF Structural Features that Control Functional Activation of CD74. Authors: Pantouris, G. / Syed, M.A. / Fan, C. / Rajasekaran, D. / Cho, T.Y. / Rosenberg, E.M. / Bucala, R. / Bhandari, V. / Lolis, E.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84.4 KB | Display | ![]() |
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PDB format | ![]() | 62.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4p01C ![]() 4p0hC ![]() 4pkzC ![]() 4pluC ![]() 4trfC ![]() 4xx7C ![]() 4xx8C ![]() 5bs9C ![]() 5bscC ![]() 5bsiC ![]() 4trs 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 0 / Auth seq-ID: 1 - 114 / Label seq-ID: 1 - 114
NCS ensembles :
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Components
#1: Protein | ![]() Mass: 12240.953 Da / Num. of mol.: 3 / Mutation: Q24A, Q25A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P14174, ![]() ![]() #2: Chemical | ![]() #3: Chemical | ![]() #4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.29 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2 M ammonium Sulphate, 3% 2-propanol,20 mM Tris.HCl pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 9, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.81→50 Å / Num. obs: 37251 / % possible obs: 98.8 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.052 / Χ2: 0.929 / Net I/av σ(I): 24.536 / Net I/σ(I): 16.2 / Num. measured all: 174375 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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Processing
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Refinement | Resolution: 1.81→47.76 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.841 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 52.96 Å2 / Biso mean: 18.459 Å2 / Biso min: 9.52 Å2
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Refinement step | Cycle: final / Resolution: 1.81→47.76 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 1.81→1.857 Å / Total num. of bins used: 20
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