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- PDB-8go5: Fungal immunomodulatory protein FIP-nha WT -

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Basic information

Entry
Database: PDB / ID: 8go5
TitleFungal immunomodulatory protein FIP-nha WT
ComponentsFungal immunomodulatory proteins
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: 2.809 Å
AuthorsLiu, Y. / Bastiaan-Net, S. / Hoppenbrouwers, T. / Li, Z.
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
D: Fungal immunomodulatory proteins
B: Fungal immunomodulatory proteins
A: Fungal immunomodulatory proteins
C: Fungal immunomodulatory proteins
E: Fungal immunomodulatory proteins
G: Fungal immunomodulatory proteins
H: Fungal immunomodulatory proteins
F: Fungal immunomodulatory proteins


Theoretical massNumber of molelcules
Total (without water)112,7338
Polymers112,7338
Non-polymers00
Water19811
1
D: Fungal immunomodulatory proteins
B: Fungal immunomodulatory proteins
A: Fungal immunomodulatory proteins
C: Fungal immunomodulatory proteins


Theoretical massNumber of molelcules
Total (without water)56,3664
Polymers56,3664
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7860 Å2
ΔGint-52 kcal/mol
Surface area20070 Å2
MethodPISA
2
E: Fungal immunomodulatory proteins
G: Fungal immunomodulatory proteins
H: Fungal immunomodulatory proteins
F: Fungal immunomodulatory proteins


Theoretical massNumber of molelcules
Total (without water)56,3664
Polymers56,3664
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8020 Å2
ΔGint-52 kcal/mol
Surface area20210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.577, 74.467, 87.473
Angle α, β, γ (deg.)99.330, 112.150, 108.590
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 through 18 or (resid 19...
21(chain B and (resid 5 through 18 or (resid 19...
31(chain C and (resid 5 through 18 or (resid 19...
41(chain D and (resid 5 through 34 or (resid 35...
51(chain E and (resid 5 through 18 or (resid 19...
61(chain F and (resid 5 through 18 or (resid 19...
71(chain G and (resid 5 through 29 or (resid 30...
81(chain H and (resid 5 through 18 or (resid 19...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNLYSLYS(chain A and (resid 5 through 18 or (resid 19...AC5 - 1810 - 23
12LYSLYSLYSLYS(chain A and (resid 5 through 18 or (resid 19...AC1924
13ASNASNLYSLYS(chain A and (resid 5 through 18 or (resid 19...AC5 - 11410 - 119
14ASNASNLYSLYS(chain A and (resid 5 through 18 or (resid 19...AC5 - 11410 - 119
15ASNASNLYSLYS(chain A and (resid 5 through 18 or (resid 19...AC5 - 11410 - 119
16ASNASNLYSLYS(chain A and (resid 5 through 18 or (resid 19...AC5 - 11410 - 119
21ASNASNLYSLYS(chain B and (resid 5 through 18 or (resid 19...BB5 - 1810 - 23
22LYSLYSLYSLYS(chain B and (resid 5 through 18 or (resid 19...BB1924
23THRTHRTRPTRP(chain B and (resid 5 through 18 or (resid 19...BB4 - 1139 - 118
24THRTHRTRPTRP(chain B and (resid 5 through 18 or (resid 19...BB4 - 1139 - 118
25THRTHRTRPTRP(chain B and (resid 5 through 18 or (resid 19...BB4 - 1139 - 118
26ARGARGARGARG(chain B and (resid 5 through 18 or (resid 19...BB3035
27ARGARGARGARG(chain B and (resid 5 through 18 or (resid 19...BB3035
28THRTHRTRPTRP(chain B and (resid 5 through 18 or (resid 19...BB4 - 1139 - 118
29THRTHRTRPTRP(chain B and (resid 5 through 18 or (resid 19...BB4 - 1139 - 118
210THRTHRTRPTRP(chain B and (resid 5 through 18 or (resid 19...BB4 - 1139 - 118
211THRTHRTRPTRP(chain B and (resid 5 through 18 or (resid 19...BB4 - 1139 - 118
31ASNASNLYSLYS(chain C and (resid 5 through 18 or (resid 19...CD5 - 1810 - 23
32LYSLYSLYSLYS(chain C and (resid 5 through 18 or (resid 19...CD1924
33THRTHRLYSLYS(chain C and (resid 5 through 18 or (resid 19...CD4 - 1149 - 119
34THRTHRLYSLYS(chain C and (resid 5 through 18 or (resid 19...CD4 - 1149 - 119
35THRTHRLYSLYS(chain C and (resid 5 through 18 or (resid 19...CD4 - 1149 - 119
37THRTHRLYSLYS(chain C and (resid 5 through 18 or (resid 19...CD4 - 1149 - 119
38THRTHRLYSLYS(chain C and (resid 5 through 18 or (resid 19...CD4 - 1149 - 119
39THRTHRLYSLYS(chain C and (resid 5 through 18 or (resid 19...CD4 - 1149 - 119
310THRTHRLYSLYS(chain C and (resid 5 through 18 or (resid 19...CD4 - 1149 - 119
311THRTHRLYSLYS(chain C and (resid 5 through 18 or (resid 19...CD4 - 1149 - 119
41ASNASNASNASN(chain D and (resid 5 through 34 or (resid 35...DA5 - 3410 - 39
42SERSERTYRTYR(chain D and (resid 5 through 34 or (resid 35...DA35 - 3640 - 41
43THRTHRLYSLYS(chain D and (resid 5 through 34 or (resid 35...DA4 - 1149 - 119
44THRTHRLYSLYS(chain D and (resid 5 through 34 or (resid 35...DA4 - 1149 - 119
45THRTHRLYSLYS(chain D and (resid 5 through 34 or (resid 35...DA4 - 1149 - 119
46THRTHRLYSLYS(chain D and (resid 5 through 34 or (resid 35...DA4 - 1149 - 119
51ASNASNLYSLYS(chain E and (resid 5 through 18 or (resid 19...EE5 - 1810 - 23
52LYSLYSLYSLYS(chain E and (resid 5 through 18 or (resid 19...EE1924
53THRTHRLYSLYS(chain E and (resid 5 through 18 or (resid 19...EE4 - 1149 - 119
54THRTHRLYSLYS(chain E and (resid 5 through 18 or (resid 19...EE4 - 1149 - 119
55THRTHRLYSLYS(chain E and (resid 5 through 18 or (resid 19...EE4 - 1149 - 119
56THRTHRLYSLYS(chain E and (resid 5 through 18 or (resid 19...EE4 - 1149 - 119
61ASNASNLYSLYS(chain F and (resid 5 through 18 or (resid 19...FH5 - 1810 - 23
62LYSLYSLYSLYS(chain F and (resid 5 through 18 or (resid 19...FH1924
63THRTHRLYSLYS(chain F and (resid 5 through 18 or (resid 19...FH4 - 1149 - 119
64THRTHRLYSLYS(chain F and (resid 5 through 18 or (resid 19...FH4 - 1149 - 119
65THRTHRLYSLYS(chain F and (resid 5 through 18 or (resid 19...FH4 - 1149 - 119
66THRTHRLYSLYS(chain F and (resid 5 through 18 or (resid 19...FH4 - 1149 - 119
71ASNASNGLYGLY(chain G and (resid 5 through 29 or (resid 30...GF5 - 2910 - 34
72ARGARGARGARG(chain G and (resid 5 through 29 or (resid 30...GF3035
73THRTHRLYSLYS(chain G and (resid 5 through 29 or (resid 30...GF4 - 1149 - 119
74THRTHRLYSLYS(chain G and (resid 5 through 29 or (resid 30...GF4 - 1149 - 119
75THRTHRLYSLYS(chain G and (resid 5 through 29 or (resid 30...GF4 - 1149 - 119
76THRTHRLYSLYS(chain G and (resid 5 through 29 or (resid 30...GF4 - 1149 - 119
81ASNASNLYSLYS(chain H and (resid 5 through 18 or (resid 19...HG5 - 1810 - 23
82LYSLYSLYSLYS(chain H and (resid 5 through 18 or (resid 19...HG1924
83THRTHRLYSLYS(chain H and (resid 5 through 18 or (resid 19...HG4 - 1149 - 119
84THRTHRLYSLYS(chain H and (resid 5 through 18 or (resid 19...HG4 - 1149 - 119
85THRTHRLYSLYS(chain H and (resid 5 through 18 or (resid 19...HG4 - 1149 - 119
87THRTHRLYSLYS(chain H and (resid 5 through 18 or (resid 19...HG4 - 1149 - 119
88THRTHRLYSLYS(chain H and (resid 5 through 18 or (resid 19...HG4 - 1149 - 119
89THRTHRLYSLYS(chain H and (resid 5 through 18 or (resid 19...HG4 - 1149 - 119
810THRTHRLYSLYS(chain H and (resid 5 through 18 or (resid 19...HG4 - 1149 - 119
811THRTHRLYSLYS(chain H and (resid 5 through 18 or (resid 19...HG4 - 1149 - 119

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Components

#1: Protein
Fungal immunomodulatory proteins


Mass: 14091.577 Da / Num. of mol.: 8
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.: 11 / 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: 3.2 Å3/Da / Density % sol: 61.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 22% PEG 1000, 0.1M Sodium citrate pH3.5, 0.2M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 25, 2021
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.809→50 Å / Num. obs: 33042 / % possible obs: 96.82 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 13.91
Reflection shellResolution: 2.809→2.85 Å / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.41 / Num. unique obs: 1675

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7WDL

7wdl


Resolution: 2.809→25.686 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 33.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.255 1640 4.97 %
Rwork0.2187 --
obs0.2206 32986 96.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.22 Å2 / Biso mean: 67.0314 Å2 / Biso min: 31.15 Å2
Refinement stepCycle: final / Resolution: 2.809→25.686 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6995 0 0 11 7006
Biso mean---63.39 -
Num. residues----886
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3914X-RAY DIFFRACTION12.316TORSIONAL
12B3914X-RAY DIFFRACTION12.316TORSIONAL
13C3914X-RAY DIFFRACTION12.316TORSIONAL
14D3914X-RAY DIFFRACTION12.316TORSIONAL
15E3914X-RAY DIFFRACTION12.316TORSIONAL
16F3914X-RAY DIFFRACTION12.316TORSIONAL
17G3914X-RAY DIFFRACTION12.316TORSIONAL
18H3914X-RAY DIFFRACTION12.316TORSIONAL
LS refinement shellResolution: 2.8091→2.8917 Å
RfactorNum. reflection% reflection
Rfree0.3024 100 -
Rwork0.3157 2273 -
obs--83 %

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