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- PDB-8go6: Fungal immunomodulatory protein FIP-nha N39A -

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Basic information

Entry
Database: PDB / ID: 8go6
TitleFungal immunomodulatory protein FIP-nha N39A
Componentsfungal immunomodulatory protein FIP-nha N39A
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: 2.813 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 N39A
A: fungal immunomodulatory protein FIP-nha N39A
C: fungal immunomodulatory protein FIP-nha N39A
D: fungal immunomodulatory protein FIP-nha N39A


Theoretical massNumber of molelcules
Total (without water)56,1944
Polymers56,1944
Non-polymers00
Water00
1
B: fungal immunomodulatory protein FIP-nha N39A
A: fungal immunomodulatory protein FIP-nha N39A

B: fungal immunomodulatory protein FIP-nha N39A
A: fungal immunomodulatory protein FIP-nha N39A


Theoretical massNumber of molelcules
Total (without water)56,1944
Polymers56,1944
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7720 Å2
ΔGint-51 kcal/mol
Surface area19240 Å2
MethodPISA
2
C: fungal immunomodulatory protein FIP-nha N39A

C: fungal immunomodulatory protein FIP-nha N39A

D: fungal immunomodulatory protein FIP-nha N39A

D: fungal immunomodulatory protein FIP-nha N39A


Theoretical massNumber of molelcules
Total (without water)56,1944
Polymers56,1944
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
crystal symmetry operation3_546x+1/2,y-1/2,z+11
crystal symmetry operation4_445-x-1/2,y-1/2,-z1
Buried area7840 Å2
ΔGint-50 kcal/mol
Surface area19220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.251, 75.284, 89.615
Angle α, β, γ (deg.)90.000, 131.550, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
fungal immunomodulatory protein FIP-nha N39A


Mass: 14048.552 Da / Num. of mol.: 4 / Mutation: 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

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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: 3.04 Å3/Da / Density % sol: 59.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M sodium chloride, 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 22, 2020
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 15619 / % possible obs: 95.3 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.061 / Rrim(I) all: 0.153 / Χ2: 1.044 / Net I/σ(I): 5.6 / Num. measured all: 97659
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.96.80.71416250.8050.2940.7730.52499.9
2.9-3.026.70.45616310.90.190.4940.57899.8
3.02-3.156.30.34916150.9320.1490.3810.67199.6
3.15-3.326.80.25716150.9690.1060.2790.71299
3.32-3.536.40.19916060.9780.0850.2170.91398.3
3.53-3.860.14715430.9840.0650.1611.10495.2
3.8-4.185.90.11315180.9890.050.1241.30392.3
4.18-4.795.60.0914340.9910.0420.11.57386.6
4.79-6.036.10.07914580.9940.0350.0871.55989
6.03-505.70.06415740.9950.0290.0711.99793

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7WDL

7wdl


Resolution: 2.813→44.807 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 26.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2506 802 5.15 %
Rwork0.197 14775 -
obs0.1998 15577 94.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.74 Å2 / Biso mean: 46.0681 Å2 / Biso min: 24.13 Å2
Refinement stepCycle: final / Resolution: 2.813→44.807 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3403 0 0 0 3403
Num. residues----434
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.813-2.98910.34481410.2719248995
2.9891-3.21980.33651470.24722566100
3.2198-3.54380.27911200.1996256898
3.5438-4.05620.17851420.1643245995
4.0562-5.10930.20181180.1586226087
5.1093-44.8070.27171340.2117243391

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