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Yorodumi- PDB-3kcw: Crystal structure of Ganoderma fungal immunomodulatory protein, GMI -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kcw | ||||||
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Title | Crystal structure of Ganoderma fungal immunomodulatory protein, GMI | ||||||
Components | immunomodulatory protein | ||||||
Keywords | IMMUNE SYSTEM / FNIII | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Ganoderma microsporum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Hsu, M.F. / Wang, A.H.J. / Yang, C.S. / Huang, C.T. / Hseu, R.S. / Lin, C.W. / Wu, M.Y. / Huang, C.S. / Fu, H.Y. | ||||||
Citation | Journal: To be Published Title: Single cysteine replacement at Leu6 increase the potent and thermostability in Ganoderma fungal immunomodulatory proteins Authors: Hsu, M.F. / Wang, A.H.J. / Yang, C.S. / Huang, C.T. / Hseu, R.S. / Lin, C.W. / Wu, M.Y. / Huang, C.S. / Fu, H.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kcw.cif.gz | 39 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kcw.ent.gz | 26.2 KB | Display | PDB format |
PDBx/mmJSON format | 3kcw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kcw_validation.pdf.gz | 409.7 KB | Display | wwPDB validaton report |
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Full document | 3kcw_full_validation.pdf.gz | 410.9 KB | Display | |
Data in XML | 3kcw_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 3kcw_validation.cif.gz | 11.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/3kcw ftp://data.pdbj.org/pub/pdb/validation_reports/kc/3kcw | HTTPS FTP |
-Related structure data
Related structure data | 1osyS S: Starting model for refinement |
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Similar 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: 15185.717 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ganoderma microsporum (fungus) / Plasmid: pPICZaA / Production host: Pichia pastoris (fungus) / Strain (production host): KM71 / References: UniProt: E7FH75*PLUS |
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#2: Water | ChemComp-HOH / |
Sequence details | A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.28 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20% PEG 4000, 0.6M NaCl, 0.1M NaMES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 23, 2007 Details: Vertically Collimating Premirror, LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator, Toroidal Focusing Mirror |
Radiation | Monochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 12868 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 9.4 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.251 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.737 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1266 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB enrty 1OSY Resolution: 2→25.85 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 320890.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.5165 Å2 / ksol: 0.337558 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→25.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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