+Open data
-Basic information
Entry | Database: PDB / ID: 5xmz | ||||||
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Title | Verticillium effector PevD1 | ||||||
Components | Effector protein PevD1 | ||||||
Keywords | SIGNALING PROTEIN / Verticillium / effector / PevD1 | ||||||
Function / homology | Alternaria alternata allergen 1 / Alternaria alternata allergen 1 / Alt a 1 (AA1)-like domain profile. / symbiont-mediated perturbation of host defense-related programmed cell death / extracellular region / Effector protein PevD1 Function and homology information | ||||||
Biological species | Verticillium dahliae (fungus) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 1.85 Å | ||||||
Authors | Liu, X. / Zhou, R. | ||||||
Citation | Journal: J. Exp. Bot. / Year: 2017 Title: The asparagine-rich protein NRP interacts with the Verticillium effector PevD1 and regulates the subcellular localization of cryptochrome 2 Authors: Zhou, R. / Zhu, T. / Han, L. / Liu, M. / Xu, M. / Liu, Y. / Han, D. / Qiu, D. / Gong, Q. / Liu, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xmz.cif.gz | 36.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xmz.ent.gz | 26.6 KB | Display | PDB format |
PDBx/mmJSON format | 5xmz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xmz_validation.pdf.gz | 429.5 KB | Display | wwPDB validaton report |
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Full document | 5xmz_full_validation.pdf.gz | 430.3 KB | Display | |
Data in XML | 5xmz_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 5xmz_validation.cif.gz | 10.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xm/5xmz ftp://data.pdbj.org/pub/pdb/validation_reports/xm/5xmz | HTTPS FTP |
-Related structure data
Similar structure data |
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-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: 16240.050 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Verticillium dahliae (fungus) / Production host: Enterobacteria phage L1 (virus) / References: UniProt: G0Y276 |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-CL / |
#4: 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: 1.97 Å3/Da / Density % sol: 37.56 % |
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Crystal grow | Temperature: 293 K / Method: batch mode / Details: 0.5M Sodium Formate, Tris pH7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: May 1, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 11198 / % possible obs: 98.4 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 15.3 |
-Processing
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Refinement | Method to determine structure: SAD / Resolution: 1.85→35.805 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 25.68
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→35.805 Å
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Refine LS restraints |
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LS refinement shell |
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