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- PDB-7wdl: Fungal immunomodulatory protein FIP-nha -

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Basic information

Entry
Database: PDB / ID: 7wdl
TitleFungal immunomodulatory protein FIP-nha
ComponentsFungal immunomodulatory protein
KeywordsIMMUNE SYSTEM / immunomodulatory / anti-tumor / tetramer
Function / homologyImmunomodulatory 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 speciesFusarium solani (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.903 Å
AuthorsLiu, 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
OrganizationGrant numberCountry
Other government2017YFD0400204 China
Other governmentKB-37-001-007 Netherlands
CitationJournal: 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
DepositionDec 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Fungal immunomodulatory protein
A: Fungal immunomodulatory protein
C: Fungal immunomodulatory protein
D: Fungal immunomodulatory protein


Theoretical massNumber of molelcules
Total (without water)55,6904
Polymers55,6904
Non-polymers00
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, static light scattering showed that FIP-nha was tetramer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8270 Å2
ΔGint-52 kcal/mol
Surface area20630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.256, 119.453, 110.224
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Fungal immunomodulatory 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 / water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.9 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 4% v/v TassimateTM pH 5.0 14% w/v PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979183 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 1.903→1.971 Å / Rmerge(I) obs: 0.416 / Num. unique obs: 5104

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
HKL-2000v7.21data reduction
HKL-2000v7.21data scaling
PHASER2.7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F3H

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
RfactorNum. reflection% reflection
Rfree0.2067 2680 5.11 %
Rwork0.1759 49746 -
obs0.1774 52426 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.38 Å2 / Biso mean: 34.4837 Å2 / Biso min: 21.08 Å2
Refinement stepCycle: final / Resolution: 1.903→26.256 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3585 0 0 400 3985
Biso mean---42.39 -
Num. residues----448
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.903-1.93750.24721240.2336250196
1.9375-1.97480.22421520.2032569100
1.9748-2.01510.21891360.19132619100
2.0151-2.05890.2431600.18742601100
2.0589-2.10670.23761440.1972582100
2.1067-2.15940.26011380.18642580100
2.1594-2.21780.24851490.19622611100
2.2178-2.2830.24791270.19092599100
2.283-2.35660.23181510.19232601100
2.3566-2.44080.20951200.19842637100
2.4408-2.53840.2211460.19152616100
2.5384-2.65390.21531430.19212609100
2.6539-2.79360.24761400.19872625100
2.7936-2.96840.19581220.18942626100
2.9684-3.19730.2181580.18352625100
3.1973-3.51830.22021320.18072657100
3.5183-4.02590.18721490.15572631100
4.0259-5.06620.16841310.1364269399
5.0662-26.2560.17911580.1728276499

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