+Open data
-Basic information
Entry | Database: PDB / ID: 8dqa | ||||||
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Title | Structure of A. thaliana MIF/D-DT-like protein-3 (MDL3) | ||||||
Components | LS1-like protein | ||||||
Keywords | CYTOKINE | ||||||
Function / homology | Macrophage migration inhibitory factor / Macrophage migration inhibitory factor (MIF) / Tautomerase/MIF superfamily / LS1-like protein Function and homology information | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Manjula, R. / Basquin, J. / Lolis, E. | ||||||
Funding support | 1items
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Citation | Journal: Sci.Signal. / Year: 2023 Title: Plant MDL proteins synergize with the cytokine MIF at CXCR2 and CXCR4 receptors in human cells. Authors: Spiller, L. / Manjula, R. / Leissing, F. / Basquin, J. / Bourilhon, P. / Sinitski, D. / Brandhofer, M. / Levecque, S. / Gerra, S. / Sabelleck, B. / Zhang, L. / Feederle, R. / Flatley, A. / ...Authors: Spiller, L. / Manjula, R. / Leissing, F. / Basquin, J. / Bourilhon, P. / Sinitski, D. / Brandhofer, M. / Levecque, S. / Gerra, S. / Sabelleck, B. / Zhang, L. / Feederle, R. / Flatley, A. / Hoffmann, A. / Panstruga, R. / Bernhagen, J. / Lolis, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dqa.cif.gz | 48.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dqa.ent.gz | 34 KB | Display | PDB format |
PDBx/mmJSON format | 8dqa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dqa_validation.pdf.gz | 410 KB | Display | wwPDB validaton report |
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Full document | 8dqa_full_validation.pdf.gz | 409.9 KB | Display | |
Data in XML | 8dqa_validation.xml.gz | 6 KB | Display | |
Data in CIF | 8dqa_validation.cif.gz | 7.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/8dqa ftp://data.pdbj.org/pub/pdb/validation_reports/dq/8dqa | HTTPS FTP |
-Related structure data
Related structure data | 8dq6C 7mrvS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 10912.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: T18N14.40, At3g51660 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9SCU2 |
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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: 2.74 Å3/Da / Density % sol: 55.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 50 mM MES, pH 6.0, 4% MPD, 0.2 M ammonium acetate, 30% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Mar 6, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→44.75 Å / Num. obs: 8229 / % possible obs: 99.96 % / Redundancy: 12.8 % / Biso Wilson estimate: 40.22 Å2 / CC1/2: 1 / Net I/σ(I): 35.38 |
Reflection shell | Resolution: 2→2.072 Å / Redundancy: 12.2 % / Mean I/σ(I) obs: 4.35 / Num. unique obs: 804 / CC1/2: 0.923 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 7MRV Resolution: 2→44.75 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.57 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→44.75 Å
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Refine LS restraints |
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LS refinement shell |
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