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Yorodumi- PDB-8uz4: Crystal Structure of macrophage migration inhibitory factor (MIF)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8uz4 | |||||||||
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Title | Crystal Structure of macrophage migration inhibitory factor (MIF) from Trichomonas vaginalis (Apo, P41212 form) | |||||||||
Components | MACROPHAGE MIGRATION INHIBITORY FACTOR | |||||||||
Keywords | CYTOKINE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / macrophage migration inhibitory factor | |||||||||
Function / homology | phenylpyruvate tautomerase / L-dopachrome isomerase / phenylpyruvate tautomerase activity / Macrophage migration inhibitory factor / Macrophage migration inhibitory factor (MIF) / Tautomerase/MIF superfamily / cytokine activity / extracellular space / L-dopachrome isomerase Function and homology information | |||||||||
Biological species | Trichomonas vaginalis (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | |||||||||
Funding support | United States, 2items
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Citation | Journal: To be published Title: Crystal Structure of macrophage migration inhibitory factor (MIF) from Trichomonas vaginalis (Apo, P41212 form) Authors: Liu, L. / Lovell, S. / Battaile, K.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8uz4.cif.gz | 147.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8uz4.ent.gz | 115.1 KB | Display | PDB format |
PDBx/mmJSON format | 8uz4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8uz4_validation.pdf.gz | 443.7 KB | Display | wwPDB validaton report |
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Full document | 8uz4_full_validation.pdf.gz | 447.9 KB | Display | |
Data in XML | 8uz4_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 8uz4_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/8uz4 ftp://data.pdbj.org/pub/pdb/validation_reports/uz/8uz4 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14842.798 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trichomonas vaginalis (eukaryote) / Strain: G3 / Gene: TVAG_219770 / Plasmid: TrvaA.00834.a.UX1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A2DXT4 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.49 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Berkeley D5: 100 mM Hepes free acid/ Sodium hydroxide pH 7.5 200 mM Ammonium acetate 25% (w/v) PEG 3350. TrvaA.00834.a.UX1.PW39224 at 35.4 mg/mL. Plate: 13617 well D5 drop 2, Puck: PSL-1907, ...Details: Berkeley D5: 100 mM Hepes free acid/ Sodium hydroxide pH 7.5 200 mM Ammonium acetate 25% (w/v) PEG 3350. TrvaA.00834.a.UX1.PW39224 at 35.4 mg/mL. Plate: 13617 well D5 drop 2, Puck: PSL-1907, Cryo: 20% PEG 200 + 80% crystallant |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Oct 9, 2023 |
Radiation | Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→80.71 Å / Num. obs: 16349 / % possible obs: 100 % / Redundancy: 23.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.02 / Rrim(I) all: 0.093 / Χ2: 1.01 / Net I/σ(I): 21.2 / Num. measured all: 379848 |
Reflection shell | Resolution: 2.4→2.46 Å / % possible obs: 100 % / Redundancy: 24.6 % / Rmerge(I) obs: 2.689 / Num. measured all: 29417 / Num. unique obs: 1195 / CC1/2: 0.627 / Rpim(I) all: 0.549 / Rrim(I) all: 2.745 / Χ2: 1.01 / Net I/σ(I) obs: 1.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→67.17 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.68 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→67.17 Å
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Refine LS restraints |
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LS refinement shell |
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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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