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Yorodumi- PDB-6fpg: Structure of the Ustilago maydis chorismate mutase 1 in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fpg | ||||||
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Title | Structure of the Ustilago maydis chorismate mutase 1 in complex with a Zea mays kiwellin | ||||||
Components |
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Keywords | CELL INVASION / Smut disease / kiwellin / chorismate | ||||||
Function / homology | Function and homology information modulation by host of symbiont process / effector-mediated suppression of host salicylic acid-mediated innate immune signaling / host apoplast / chorismate metabolic process / chorismate mutase / chorismate mutase activity / apoplast / enzyme inhibitor activity / host cell cytosol / aromatic amino acid family biosynthetic process ...modulation by host of symbiont process / effector-mediated suppression of host salicylic acid-mediated innate immune signaling / host apoplast / chorismate metabolic process / chorismate mutase / chorismate mutase activity / apoplast / enzyme inhibitor activity / host cell cytosol / aromatic amino acid family biosynthetic process / defense response to fungus / extracellular region Similarity search - Function | ||||||
Biological species | Ustilago maydis (fungus) Zea mays (maize) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Altegoer, F. / Steinchen, W. / Bange, G. | ||||||
Citation | Journal: Nature / Year: 2019 Title: A kiwellin disarms the metabolic activity of a secreted fungal virulence factor. Authors: Han, X. / Altegoer, F. / Steinchen, W. / Binnebesel, L. / Schuhmacher, J. / Glatter, T. / Giammarinaro, P.I. / Djamei, A. / Rensing, S.A. / Reissmann, S. / Kahmann, R. / Bange, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fpg.cif.gz | 661.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fpg.ent.gz | 544.5 KB | Display | PDB format |
PDBx/mmJSON format | 6fpg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/6fpg ftp://data.pdbj.org/pub/pdb/validation_reports/fp/6fpg | HTTPS FTP |
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-Related structure data
Related structure data | 6fpfSC 6h3pC 6hjwC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31060.238 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ustilago maydis (strain 521 / FGSC 9021) (fungus) Gene: UMAG_05731 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0D1DWQ2 #2: Protein | Mass: 18772.604 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zea mays (maize) / Gene: 103626138, ZEAMMB73_Zm00001d013945 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1D6GNR3 #3: Chemical | ChemComp-CIT / #4: 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: 2.57 Å3/Da / Density % sol: 52.06 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M sodium citrate pH 5.5, 15 % (w/v) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→49 Å / Num. obs: 168279 / % possible obs: 96.6 % / Redundancy: 2.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.041 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 16605 / CC1/2: 0.7 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6FPF Resolution: 1.8→48.497 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.08
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→48.497 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 30.9881 Å / Origin y: -6.8305 Å / Origin z: -14.7153 Å
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Refinement TLS group | Selection details: all |