+Open data
-Basic information
Entry | Database: PDB / ID: 5zc3 | ||||||
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Title | The Crystal Structure of PcRxLR12 | ||||||
Components | RxLR effector | ||||||
Keywords | IMMUNOSUPPRESSANT / RxLR effectors | ||||||
Function / homology | RxLR effector Function and homology information | ||||||
Biological species | Phytophthora capsici (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.005 Å | ||||||
Authors | Zhao, L. / Zhang, X. / Zhu, C. | ||||||
Funding support | China, 1items
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Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2018 Title: Crystal structure of the RxLR effector PcRxLR12 from Phytophthora capsici Authors: Zhao, L. / Zhang, X. / Zhang, X. / Song, W. / Li, X. / Feng, R. / Yang, C. / Huang, Z. / Zhu, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zc3.cif.gz | 322.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zc3.ent.gz | 273.6 KB | Display | PDB format |
PDBx/mmJSON format | 5zc3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zc/5zc3 ftp://data.pdbj.org/pub/pdb/validation_reports/zc/5zc3 | HTTPS FTP |
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-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
#1: Protein | Mass: 53555.082 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phytophthora capsici (eukaryote) / Strain: SD33 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A3F2YLV0*PLUS |
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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: 2.14 Å3/Da / Density % sol: 42.68 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100mM HEPES pH 7.5, 6%(w/v) PEG 6000 and 5%(v/v) -2-methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9796 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 3→47 Å / Num. obs: 19409 / % possible obs: 99.8 % / Redundancy: 7.1 % / Net I/σ(I): 32.3 |
Reflection shell | Resolution: 3→3.1 Å / Redundancy: 6.9 % / Num. unique obs: 1622 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.005→47 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.74
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.005→47 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS params. | Method: refined / Origin x: 137.2092 Å / Origin y: 79.698 Å / Origin z: 196.3175 Å
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Refinement TLS group | Selection details: all |