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- PDB-3kcw: Crystal structure of Ganoderma fungal immunomodulatory protein, GMI -

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Basic information

Entry
Database: PDB / ID: 3kcw
TitleCrystal structure of Ganoderma fungal immunomodulatory protein, GMI
Componentsimmunomodulatory protein
KeywordsIMMUNE SYSTEM / FNIII
Function / homology
Function and homology information


regulation of immune system process / carbohydrate binding
Similarity search - Function
Fungal immunomodulatory protein Fve / Immunomodulatory protein FIP-Fve, fungal / Fungal immunomodulatory protein FIP-Fve superfamily / Fungal immunomodulatory protein Fve / : / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunomodulatory protein
Similarity search - Component
Biological speciesGanoderma microsporum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHsu, M.F. / Wang, A.H.J. / Yang, C.S. / Huang, C.T. / Hseu, R.S. / Lin, C.W. / Wu, M.Y. / Huang, C.S. / Fu, H.Y.
CitationJournal: To be Published
Title: Single cysteine replacement at Leu6 increase the potent and thermostability in Ganoderma fungal immunomodulatory proteins
Authors: Hsu, M.F. / Wang, A.H.J. / Yang, C.S. / Huang, C.T. / Hseu, R.S. / Lin, C.W. / Wu, M.Y. / Huang, C.S. / Fu, H.Y.
History
DepositionOct 22, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: immunomodulatory protein


Theoretical massNumber of molelcules
Total (without water)15,1861
Polymers15,1861
Non-polymers00
Water2,918162
1
A: immunomodulatory protein

A: immunomodulatory protein


Theoretical massNumber of molelcules
Total (without water)30,3712
Polymers30,3712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-x,-y,z1
Buried area2810 Å2
ΔGint-26 kcal/mol
Surface area11330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.734, 95.734, 80.072
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-513-

HOH

21A-592-

HOH

31A-593-

HOH

41A-596-

HOH

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Components

#1: Protein immunomodulatory protein


Mass: 15185.717 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ganoderma microsporum (fungus) / Plasmid: pPICZaA / Production host: Pichia pastoris (fungus) / Strain (production host): KM71 / References: UniProt: E7FH75*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 3.02 Å3/Da / Density % sol: 59.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG 4000, 0.6M NaCl, 0.1M NaMES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 23, 2007
Details: Vertically Collimating Premirror, LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator, Toroidal Focusing Mirror
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 12868 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 9.4 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.251
Reflection shellResolution: 2→2.07 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.737 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1266 / % possible all: 100

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Processing

Software
NameClassification
Blu-Icedata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB enrty 1OSY

1osy


Resolution: 2→25.85 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 320890.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.212 629 5.1 %RANDOM
Rwork0.189 ---
all0.19 12882 --
obs0.189 12410 96.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.5165 Å2 / ksol: 0.337558 e/Å3
Displacement parametersBiso mean: 32 Å2
Baniso -1Baniso -2Baniso -3
1-1.76 Å20 Å20 Å2
2--1.76 Å20 Å2
3----3.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2→25.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms870 0 0 162 1032
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_improper_angle_d0.62
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it1.982
X-RAY DIFFRACTIONc_scbond_it2.32
X-RAY DIFFRACTIONc_scangle_it3.42.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.253 102 5.3 %
Rwork0.228 1812 -
obs--90.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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