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- PDB-1osy: Crystal structure of FIP-Fve fungal immunomodulatory protein -

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Basic information

Entry
Database: PDB / ID: 1osy
TitleCrystal structure of FIP-Fve fungal immunomodulatory protein
ComponentsIMMUNOMODULATORY PROTEIN FIP-FVEImmunotherapy
KeywordsSUGAR BINDING PROTEIN / IMMUNE SYSTEM / fungal protein / immunomodulatory / fibronectin fold / hemagglutination / lectin
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
BROMIDE ION / Immunomodulatory protein FIP-Fve
Similarity search - Component
Biological speciesFlammulina velutipes (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsPalasingam, P. / Joseph, J.S. / Seow, S.V. / Shai, V. / Robinson, H. / Chua, K.Y. / Kolatkar, P.R.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: A 1.7A structure of Fve, a member of the new fungal immunomodulatory protein family
Authors: Paaventhan, P. / Joseph, J.S. / Seow, S.V. / Vaday, S. / Robinson, H. / Chua, K.Y. / Kolatkar, P.R.
History
DepositionMar 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IMMUNOMODULATORY PROTEIN FIP-FVE
B: IMMUNOMODULATORY PROTEIN FIP-FVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,76118
Polymers25,4822
Non-polymers1,27816
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-34 kcal/mol
Surface area11280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.118, 97.118, 61.413
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Cell settingtetragonal
Space group name H-MP43212

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Components

#1: Protein IMMUNOMODULATORY PROTEIN FIP-FVE / Immunotherapy


Mass: 12741.241 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Flammulina velutipes (fungus) / References: UniProt: P80412
#2: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.67 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 400, ammonium sulfate, Tris-base, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.5 %(w/v)PEG4001reservoir
22.0 Mammonium sulfate1reservoir
30.1 MTris base1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9202 Å
DetectorType: PHILLIPS / Detector: CCD / Date: Mar 7, 2002
RadiationMonochromator: Si III Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 32880 / Num. obs: 32880 / % possible obs: 99.96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Biso Wilson estimate: 15.319 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 28.1
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 16.7 / Num. unique all: 3249 / % possible all: 100
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 30 Å / % possible obs: 100 % / Num. measured all: 464964
Reflection shell
*PLUS
% possible obs: 100 % / Num. unique obs: 3249

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
REFMAC5refinement
RefinementMethod to determine structure: SAD / Resolution: 1.7→30.02 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.208 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21016 1650 5.1 %RANDOM
Rwork0.18218 ---
all0.18358 32880 --
obs0.18358 30783 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.666 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1788 0 16 136 1940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221830
X-RAY DIFFRACTIONr_bond_other_d0.0010.021593
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.9412490
X-RAY DIFFRACTIONr_angle_other_deg0.92133724
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8993224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.84415311
X-RAY DIFFRACTIONr_chiral_restr0.2310.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022026
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02374
X-RAY DIFFRACTIONr_nbd_refined0.2710.3327
X-RAY DIFFRACTIONr_nbd_other0.2120.31447
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.5131
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.310.38
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2910.317
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.514
X-RAY DIFFRACTIONr_mcbond_it0.8981.51124
X-RAY DIFFRACTIONr_mcangle_it1.60321827
X-RAY DIFFRACTIONr_scbond_it2.2923706
X-RAY DIFFRACTIONr_scangle_it3.8394.5663
LS refinement shellResolution: 1.7→1.745 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.197 114
Rwork0.16 2183
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3236-0.4538-0.1061.6346-0.11340.03190.06680.03170.0266-0.0158-0.0508-0.0656-0.01110.0027-0.0160.08260.00850.01180.05280.00660.002231.83834.41315.954
20.0923-0.1092-0.11350.6926-0.0160.14270.00960.0276-0.0212-0.0046-0.03270.0279-0.0061-0.00950.02310.06380.0019-0.00640.0608-0.00550.022733.7582.51518.421
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1131 - 113
2X-RAY DIFFRACTION2BB1 - 1121 - 112
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.21 / Rfactor Rwork: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.466

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