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- PDB-7wdm: Fungal immunomodulatory protein FIP-gmi -

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Basic information

Entry
Database: PDB / ID: 7wdm
TitleFungal immunomodulatory protein FIP-gmi
ComponentsImmunomodulatory 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
Function and homology information
Biological speciesGanoderma microsporum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.123 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: To Be Published
Title: Linking the thermostability of FIP-nha (Nectria haematococca) to its structural properties
Authors: Liu, Y.
History
DepositionDec 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 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
A: Immunomodulatory protein


Theoretical massNumber of molelcules
Total (without water)14,7681
Polymers14,7681
Non-polymers00
Water2,306128
1
A: Immunomodulatory protein

A: Immunomodulatory protein

A: Immunomodulatory protein

A: Immunomodulatory protein


Theoretical massNumber of molelcules
Total (without water)59,0734
Polymers59,0734
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_553-y,-x,-z-21
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_553y,x,-z-21
Buried area9290 Å2
ΔGint-77 kcal/mol
Surface area19760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.585, 96.585, 80.303
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-205-

HOH

21A-208-

HOH

31A-216-

HOH

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Components

#1: Protein Immunomodulatory 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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 3.17 Å3/Da / Density % sol: 61.2 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 0.1 M Na3Citrate (pH 5.6) 0.5 M NH4H2PO4

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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 EIGER X 16M / Detector: PIXEL / Date: Jul 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.124→2.199 Å / Rmerge(I) obs: 0.915 / Num. unique obs: 1006

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
HKL-20007.21data reduction
HKL-20007.21data scaling
PHASER2.7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F3H

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
RfactorNum. reflection% reflection
Rfree0.2173 514 4.93 %
Rwork0.2055 9920 -
obs0.2061 10434 94.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.47 Å2 / Biso mean: 35.6297 Å2 / Biso min: 25.06 Å2
Refinement stepCycle: final / Resolution: 2.123→38.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms885 0 0 128 1013
Biso mean---41.9 -
Num. residues----113
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.123-2.33620.28471250.2661241694
2.3362-2.67420.30371250.2664241494
2.6742-3.36890.21221250.2055243293
3.3689-38.040.18671390.1687265897

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