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- PDB-1ofz: Crystal structure of fungal lectin : six-bladed beta-propeller fo... -

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Basic information

Entry
Database: PDB / ID: 1ofz
TitleCrystal structure of fungal lectin : six-bladed beta-propeller fold and novel fucose recognition mode for aleuria aurantia lectin
ComponentsFUCOSE-SPECIFIC LECTIN
KeywordsSUGAR BINDING PROTEIN / SUGAR-BINDING PROTEIN / LECTIN / AAL / FUCOSE / ALEURIA AURANTIA LECTIN
Function / homology
Function and homology information


reproductive fruiting body development / fucose binding / defense response to fungus / carbohydrate binding / protein homodimerization activity / identical protein binding
Similarity search - Function
Fucose-specific lectin / Fucose-specific lectin / Fungal fucose-specific lectin / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
alpha-L-fucopyranose / beta-L-fucopyranose / Fucose-specific lectin
Similarity search - Component
Biological speciesALEURIA AURANTIA (orange peel mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.5 Å
AuthorsWimmerova, M. / Mitchell, E. / Sanchez, J.F. / Gautier, C. / Imberty, A.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal Structure of Fungal Lectin: Six-Bladed {Beta}-Propeller Fold and Novel Fucose Recognition Mode for Aleuria Aurantia Lectin
Authors: Wimmerova, M. / Mitchell, E. / Sanchez, J.F. / Gautier, C. / Imberty, A.
History
DepositionApr 22, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FUCOSE-SPECIFIC LECTIN
B: FUCOSE-SPECIFIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,87814
Polymers66,9082
Non-polymers1,97012
Water21,0051166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint21.15 kcal/mol
Surface area23920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.969, 86.406, 77.849
Angle α, β, γ (deg.)90.00, 90.62, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.6857, 0.6241, 0.3745), (0.6177, 0.2269, 0.7529), (0.385, 0.7476, -0.5411)
Vector: 21.6401, -43.8932, 54.1108)

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Components

#1: Protein FUCOSE-SPECIFIC LECTIN / ALEURIA AURANTIA LECTIN


Mass: 33454.039 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ALEURIA AURANTIA (orange peel mushroom) / References: UniProt: P18891
#2: Sugar
ChemComp-FUL / beta-L-fucopyranose / 6-DEOXY-BETA-L-GALACTOSE / Fucose


Type: L-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-fucopyranoseCOMMON NAMEGMML 1.0
b-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar
ChemComp-FUC / alpha-L-fucopyranose / Fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1166 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsP18891 HAS RESIDUE 139 AS GLY AND 163 AS VAL. ELECTRON DENSITY OF MOLECULE CRYSTALLISED INDICATES ...P18891 HAS RESIDUE 139 AS GLY AND 163 AS VAL. ELECTRON DENSITY OF MOLECULE CRYSTALLISED INDICATES 139 LEU AND 163 ALA

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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: 2.2 Å3/Da / Density % sol: 32.8 %
Description: DATA WERE COLLECTED AT ENERGY REMOTE FROM THE MERCURY ANOMALOUS EDGE
Crystal growpH: 6.5
Details: 2UL BUFFER (0.1 M SODIUM CACODYLATE PH 6.5, 0.2M MAGNESIUM ACETATE TETRAHYDRATE, 20% PEG 8000) PLUS 2UL OF LECTIN PROTEIN AT 10 MG/ML AND L-FUCOSE AT 137 UG/ML
Crystal
*PLUS
Density Matthews: 2.2 Å3/Da / Density % sol: 46 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 Msodium cacodylate1reservoirpH6.5
20.2 Mmagnesium acetate tetrahydrate1reservoir
320 %PEG80001reservoir
410 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 15, 2003 / Details: MULTILAYER
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.5→19.96 Å / Num. obs: 534572 / % possible obs: 96.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 8.4
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 18.4 / % possible all: 96.8
Reflection
*PLUS
Highest resolution: 1.5 Å / Num. obs: 94102 / Redundancy: 3.6 % / Num. measured all: 534572 / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
Highest resolution: 1.5 Å / % possible obs: 96.8 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
MOSFLMdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: OTHER / Resolution: 1.5→19.96 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.417 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY WITH OCCUPANCY SET TO ZERO.
RfactorNum. reflection% reflectionSelection details
Rfree0.179 1884 2 %RANDOM
Rwork0.144 ---
obs-92216 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 12.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4742 0 132 1166 6040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0215180
X-RAY DIFFRACTIONr_bond_other_d0.0160.024424
X-RAY DIFFRACTIONr_angle_refined_deg1.541.9357100
X-RAY DIFFRACTIONr_angle_other_deg1.439310287
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0965664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0990.2773
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025897
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021100
X-RAY DIFFRACTIONr_nbd_refined0.1950.2859
X-RAY DIFFRACTIONr_nbd_other0.2770.25644
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0930.22889
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2907
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2890.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.275
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8581.53192
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.44825113
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.95431961
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9564.51953
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.279 107
Rwork0.262 5241
Refinement
*PLUS
Num. reflection obs: 92218
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.556
X-RAY DIFFRACTIONr_plane_restr0.008
X-RAY DIFFRACTIONr_chiral_restr0.165
LS refinement shell
*PLUS
Rfactor Rfree: 0.273 / Rfactor Rwork: 0.263 / Num. reflection Rwork: 5239

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