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- PDB-8go7: Fungal immunomodulatory protein FIP-nha N5+39A -

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Basic information

Entry
Database: PDB / ID: 8go7
TitleFungal immunomodulatory protein FIP-nha N5+39A
ComponentsFungal immunomodulatory protein FIP-nha
KeywordsIMMUNE SYSTEM / immunomodulatory / anti-tumor / thermostable / hydrolysis resistance
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 haematococcum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.303 Å
AuthorsLiu, Y. / Bastiaan-Net, S. / Hoppenbrouwers, T. / Li, Z. / Wichers, H.J.
Funding support China, Netherlands, 2items
OrganizationGrant numberCountry
Other government2017YFD0400204 China
Other governmentKB-37-001-007 Netherlands
CitationJournal: Molecules / Year: 2023
Title: Glycosylation Contributes to Thermostability and Proteolytic Resistance of rFIP-nha ( Nectria haematococca ).
Authors: Liu, Y. / Hoppenbrouwers, T. / Wang, Y. / Xie, Y. / Wei, X. / Zhang, H. / Du, G. / Imam, K.M.S.U. / Wichers, H. / Li, Z. / Bastiaan-Net, S.
History
DepositionAug 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Fungal immunomodulatory protein FIP-nha
A: Fungal immunomodulatory protein FIP-nha
C: Fungal immunomodulatory protein FIP-nha
D: Fungal immunomodulatory protein FIP-nha


Theoretical massNumber of molelcules
Total (without water)56,0224
Polymers56,0224
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, tetramer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7850 Å2
ΔGint-52 kcal/mol
Surface area19170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.311, 101.304, 74.877
Angle α, β, γ (deg.)90.000, 129.190, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Fungal immunomodulatory protein FIP-nha


Mass: 14005.526 Da / Num. of mol.: 4 / Mutation: N5A,N39A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium haematococcum (fungus)
Strain: ATCC MYA-4622 / CBS 123669 / FGSC 9596 / NRRL 45880 / 77-13-4
Gene: NECHADRAFT_88285 / Production host: Komagataella pastoris (fungus) / References: UniProt: C7ZE17
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 3.1 Å3/Da / Density % sol: 60.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Sodium choride, 0.1M Bis-Tris pH 6.5, 1.5M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 29149 / % possible obs: 96.3 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.055 / Rrim(I) all: 0.136 / Χ2: 1.055 / Net I/σ(I): 9.2 / Num. measured all: 182087
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.346.30.44115240.9160.190.4810.611100
2.34-2.386.70.40914760.9540.1690.4440.644100
2.38-2.4370.35515530.9660.1440.3830.696100
2.43-2.486.90.32114800.9660.1310.3470.824100
2.48-2.536.90.29514770.9660.120.3190.834100
2.53-2.596.70.25315320.9640.1050.2750.90199.9
2.59-2.666.10.25914790.40.1180.2861.29599.6
2.66-2.735.90.34114980.7680.1610.3782.09299.7
2.73-2.816.80.17715210.9790.0730.1921.17899.8
2.81-2.96.70.16614970.9790.0690.181.22599.3
2.9-36.50.13914900.9830.0590.1521.30798.9
3-3.126.30.13115200.9840.0570.1431.2198.2
3.12-3.265.80.11614340.9860.0520.1280.92396.4
3.26-3.445.80.1514280.8780.0690.1661.43495.8
3.44-3.655.60.13413840.8330.0610.1481.48391.1
3.65-3.935.40.13713250.9150.0650.1520.91887.5
3.93-4.335.30.09312750.9830.0430.1030.9183.1
4.33-4.955.60.07512890.9920.0340.0820.92785.4
4.95-6.245.90.0914410.9830.040.0990.90294
6.24-506.20.11715260.9880.0510.1280.99998.3

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-30007.21data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASER2.7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7WDL

7wdl


Resolution: 2.303→28.981 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2603 1451 4.99 %
Rwork0.2234 27654 -
obs0.2254 29105 96.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.18 Å2 / Biso mean: 54.4009 Å2 / Biso min: 38.34 Å2
Refinement stepCycle: final / Resolution: 2.303→28.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3370 0 0 103 3473
Biso mean---54.19 -
Num. residues----428
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.303-2.38520.33421280.2724279098
2.3852-2.48070.33441860.26262875100
2.4807-2.59350.42391390.2882869100
2.5935-2.73020.3261680.2981281799
2.7302-2.90110.31691340.28142878100
2.9011-3.12480.30891370.2556287099
3.1248-3.43880.27411370.2424274196
3.4388-3.93540.25141160.2031259589
3.9354-4.95410.20371530.1711241784
4.9541-28.9810.21721530.1984280296

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