+Open data
-Basic information
Entry | Database: PDB / ID: 7wdl | |||||||||
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Title | Fungal immunomodulatory protein FIP-nha | |||||||||
Components | Fungal immunomodulatory protein | |||||||||
Keywords | IMMUNE SYSTEM / immunomodulatory / anti-tumor / tetramer | |||||||||
Function / homology | Immunomodulatory protein FIP-Fve, fungal / Fungal immunomodulatory protein FIP-Fve superfamily / Fungal immunomodulatory protein Fve / regulation of immune system process / carbohydrate binding / Immunomodulatory protein Ling Zhi-8 Function and homology information | |||||||||
Biological species | Fusarium solani (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.903 Å | |||||||||
Authors | Liu, Y. / Bastiaan-Net, S. / Zhang, Y. / Hoppenbrouwers, T. / Xie, Y. / Wang, Y. / Wei, X. / Du, G. / Zhang, H. / Imam, K.M.S.U. ...Liu, Y. / Bastiaan-Net, S. / Zhang, Y. / Hoppenbrouwers, T. / Xie, Y. / Wang, Y. / Wei, X. / Du, G. / Zhang, H. / Imam, K.M.S.U. / Wichers, H.J. / Li, Z. | |||||||||
Funding support | China, Netherlands, 2items
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Citation | Journal: Int.J.Biol.Macromol. / Year: 2022 Title: Linking the thermostability of FIP-nha (Nectria haematococca) to its structural properties. Authors: Liu, Y. / Bastiaan-Net, S. / Zhang, Y. / Hoppenbrouwers, T. / Xie, Y. / Wang, Y. / Wei, X. / Du, G. / Zhang, H. / Imam, K.M.D.S.U. / Wichers, H. / Li, Z. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wdl.cif.gz | 109.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wdl.ent.gz | 82.9 KB | Display | PDB format |
PDBx/mmJSON format | 7wdl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wdl_validation.pdf.gz | 442.8 KB | Display | wwPDB validaton report |
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Full document | 7wdl_full_validation.pdf.gz | 444.3 KB | Display | |
Data in XML | 7wdl_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | 7wdl_validation.cif.gz | 32 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/7wdl ftp://data.pdbj.org/pub/pdb/validation_reports/wd/7wdl | HTTPS FTP |
-Related structure data
Related structure data | 3f3hS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13922.395 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fusarium solani (fungus) Strain: ATCC MYA-4622 / CBS 123669 / FGSC 9596 / NRRL 45880 / 77-13-4 Gene: NECHADRAFT_88285 / Production host: Escherichia coli (E. coli) / References: UniProt: C7ZE17 #2: 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: 2.99 Å3/Da / Density % sol: 58.9 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 4% v/v TassimateTM pH 5.0 14% w/v PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979183 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979183 Å / Relative weight: 1 |
Reflection | Resolution: 1.903→26.256 Å / Num. obs: 52430 / % possible obs: 99.8 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 25.57 |
Reflection shell | Resolution: 1.903→1.971 Å / Rmerge(I) obs: 0.416 / Num. unique obs: 5104 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3F3H Resolution: 1.903→26.256 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.74 / 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: 70.38 Å2 / Biso mean: 34.4837 Å2 / Biso min: 21.08 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.903→26.256 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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