+Open data
-Basic information
Entry | Database: PDB / ID: 3fwt | ||||||
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Title | Crystal structure of Leishmania major MIF2 | ||||||
Components | Macrophage migration inhibitory factor-like protein | ||||||
Keywords | CYTOKINE / homotrimer / tautomerase | ||||||
Function / homology | Function and homology information phenylpyruvate tautomerase / L-dopachrome isomerase / phenylpyruvate tautomerase activity / cytokine activity / extracellular space Similarity search - Function | ||||||
Biological species | Leishmania major (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Walkinshaw, M.D. / Richardson, J.M. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2009 Title: Structures of Leishmania major orthologues of macrophage migration inhibitory factor Authors: Richardson, J.M. / Morrison, L.S. / Bland, N.D. / Bruce, S. / Coombs, G.H. / Mottram, J.C. / Walkinshaw, M.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fwt.cif.gz | 37.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fwt.ent.gz | 25.4 KB | Display | PDB format |
PDBx/mmJSON format | 3fwt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fwt_validation.pdf.gz | 437.9 KB | Display | wwPDB validaton report |
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Full document | 3fwt_full_validation.pdf.gz | 441.8 KB | Display | |
Data in XML | 3fwt_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 3fwt_validation.cif.gz | 11 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fw/3fwt ftp://data.pdbj.org/pub/pdb/validation_reports/fw/3fwt | HTTPS FTP |
-Related structure data
Related structure data | 3fwuC 1uizS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 14769.774 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania major (eukaryote) / Strain: Friedlin / Gene: LmjF33.1750 / Plasmid: pet28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4Q412 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.77 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 29% w/v PEG4000 and 100mM Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.931 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 6, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→38.8 Å / Num. all: 10155 / Num. obs: 10155 / % possible obs: 100 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.089 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 5.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1UIZ Resolution: 1.9→34.73 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.874 / SU B: 4.056 / SU ML: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
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Solvent computation | Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.23 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→34.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å
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