+Open data
-Basic information
Entry | Database: PDB / ID: 7wdm | |||||||||
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Title | Fungal immunomodulatory protein FIP-gmi | |||||||||
Components | 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 Function and homology information | |||||||||
Biological species | Ganoderma microsporum (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.123 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: To Be Published Title: Linking the thermostability of FIP-nha (Nectria haematococca) to its structural properties Authors: Liu, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wdm.cif.gz | 40.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wdm.ent.gz | 25.2 KB | Display | PDB format |
PDBx/mmJSON format | 7wdm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wdm_validation.pdf.gz | 407.7 KB | Display | wwPDB validaton report |
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Full document | 7wdm_full_validation.pdf.gz | 407.6 KB | Display | |
Data in XML | 7wdm_validation.xml.gz | 7.5 KB | Display | |
Data in CIF | 7wdm_validation.cif.gz | 10.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/7wdm ftp://data.pdbj.org/pub/pdb/validation_reports/wd/7wdm | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 14768.290 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ganoderma microsporum (fungus) / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / References: UniProt: E7FH75 |
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#2: 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: 3.17 Å3/Da / Density % sol: 61.2 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 0.1 M Na3Citrate (pH 5.6) 0.5 M NH4H2PO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 9, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.123→38.04 Å / Num. obs: 10434 / % possible obs: 94.52 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 34.41 |
Reflection shell | Resolution: 2.124→2.199 Å / Rmerge(I) obs: 0.915 / Num. unique obs: 1006 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3F3H Resolution: 2.123→38.04 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.53 / 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: 64.47 Å2 / Biso mean: 35.6297 Å2 / Biso min: 25.06 Å2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.123→38.04 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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