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- PDB-2wkf: Crystal Structure of Macrophage Migration Inhibitory Factor from ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2wkf | ||||||
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Title | Crystal Structure of Macrophage Migration Inhibitory Factor from Plasmodium falciparum | ||||||
![]() | (MACROPHAGE MIGRATION INHIBITORY FACTOR) x 2 | ||||||
![]() | CYTOKINE | ||||||
Function / homology | ![]() Maurer's cleft / Neutrophil degranulation / phenylpyruvate tautomerase / phenylpyruvate tautomerase activity / evasion of host immune response / cytokine activity / host cell cytoplasm / oxidoreductase activity / host cell surface receptor binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dobson, S.E. / Augustijn, K.D. / Brannigan, J.A. / Dodson, E.J. / Waters, A.P. / Wilkinson, A.J. | ||||||
![]() | ![]() Title: The crystal structures of macrophage migration inhibitory factor from Plasmodium falciparum and Plasmodium berghei. Authors: Dobson, S.E. / Augustijn, K.D. / Brannigan, J.A. / Schnick, C. / Janse, C.J. / Dodson, E.J. / Waters, A.P. / Wilkinson, A.J. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.3 KB | Display | ![]() |
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PDB format | ![]() | 40.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.2 KB | Display | ![]() |
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Full document | ![]() | 453.9 KB | Display | |
Data in XML | ![]() | 11.2 KB | Display | |
Data in CIF | ![]() | 14.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2wkbSC 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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.262, -0.4478, -0.8549), Vector: |
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Components
#1: Protein | Mass: 13940.556 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-116 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 3D7 / Plasmid: PQE-70 / Production host: ![]() ![]() | ||
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#2: Protein | Mass: 14016.674 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-116 Source method: isolated from a genetically manipulated source Details: CYS2 IS MODIFIED TO CME IN CHAIN B DUE TO BINDING TO BETA-MERCAPTOETHANOL Source: (gene. exp.) ![]() ![]() Strain: 3D7 / Plasmid: PQE-70 / Production host: ![]() ![]() | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.63 % / Description: NONE |
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Crystal grow | pH: 8 Details: 10% PEG 1000, 10% PEG 8000, 0.2 M KSCN, 0.1 M TRIS-HCL PH 8.0 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 24, 2006 / Details: MIRRORS |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 12419 / % possible obs: 99.9 % / Observed criterion σ(I): 5 / Redundancy: 14.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 34.6 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 6.1 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2WKB Resolution: 2.05→58.9 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.885 / SU B: 16.881 / SU ML: 0.2 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.311 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES RESIDUAL ONLY
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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: 32.002 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→58.9 Å
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Refine LS restraints |
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