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Yorodumi- PDB-7jmr: Crystal structure of the pea pathogenicity protein 2 from Madurel... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jmr | ||||||
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Title | Crystal structure of the pea pathogenicity protein 2 from Madurella mycetomatis | ||||||
Components | Pea pathogenicity protein 2 | ||||||
Keywords | LYASE / Gallic acid decarboxylase | ||||||
Function / homology | SnoaL-like domain / SnoaL-like domain / WW/rsp5/WWP domain profile. / WW domain / NTF2-like domain superfamily / : / Pea pathogenicity protein 2 Function and homology information | ||||||
Biological species | Madurella mycetomatis (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.67 Å | ||||||
Authors | Zeug, M. / Markovic, N. / Iancu, C.V. / Tripp, J. / Oreb, M. / Choe, J. | ||||||
Citation | Journal: Sci Rep / Year: 2021 Title: Crystal structures of non-oxidative decarboxylases reveal a new mechanism of action with a catalytic dyad and structural twists. Authors: Zeug, M. / Markovic, N. / Iancu, C.V. / Tripp, J. / Oreb, M. / Choe, J.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jmr.cif.gz | 96.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jmr.ent.gz | 78.5 KB | Display | PDB format |
PDBx/mmJSON format | 7jmr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jm/7jmr ftp://data.pdbj.org/pub/pdb/validation_reports/jm/7jmr | HTTPS FTP |
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-Related 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: 27641.273 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Madurella mycetomatis (fungus) / Gene: MMYC01_201259, MMYC01_203104 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A175WC91 | ||||
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#2: Chemical | ChemComp-K / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.39 Å3/Da / Density % sol: 63.75 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 15 % PEG 3350, 0.2 M Calcium Chloride, 0.1 M MES / PH range: 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 4, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→38.74 Å / Num. obs: 78547 / % possible obs: 99.5 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 40 |
Reflection shell | Resolution: 1.67→1.69 Å / Num. unique obs: 2702 / Rsym value: 0.704 / % possible all: 96 |
-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.67→38.74 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0.63 / Phase error: 19.15 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.31 Å2 / Biso mean: 35.6067 Å2 / Biso min: 17.87 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.67→38.74 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28
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