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- PDB-2r0f: Ligand free structure of fungal lectin CGL3 -

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Basic information

Entry
Database: PDB / ID: 2r0f
TitleLigand free structure of fungal lectin CGL3
ComponentsCGL3 lectin
KeywordsSUGAR BINDING PROTEIN / galectin-related / lectin / chitooligosaccharides
Function / homology
Function and homology information


carbohydrate binding / extracellular region
Similarity search - Function
Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesCoprinus cinereus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWaelti, M.A. / Walser, P.J. / Thore, S. / Gruenler, A. / Ban, N. / Kuenzler, M. / Aebi, M.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural Basis for Chitotetraose Coordination by CGL3, a Novel Galectin-Related Protein from Coprinopsis cinerea
Authors: Waelti, M.A. / Walser, P.J. / Thore, S. / Gruenler, A. / Bednar, M. / Kuenzler, M. / Aebi, M.
History
DepositionAug 19, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CGL3 lectin
B: CGL3 lectin


Theoretical massNumber of molelcules
Total (without water)37,5172
Polymers37,5172
Non-polymers00
Water4,288238
1
A: CGL3 lectin
B: CGL3 lectin

A: CGL3 lectin
B: CGL3 lectin


Theoretical massNumber of molelcules
Total (without water)75,0334
Polymers75,0334
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Buried area7920 Å2
ΔGint-33.8 kcal/mol
Surface area27040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.375, 112.375, 175.664
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 6 / Auth seq-ID: 1 - 163 / Label seq-ID: 1 - 163

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein CGL3 lectin


Mass: 18758.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coprinus cinereus (fungus) / Strain: AmutBmut / Gene: cgl3 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q206Z5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 4.27 Å3/Da / Density % sol: 71.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: MPD, sodium citrate, pH4.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.966 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 12, 2005
RadiationMonochromator: Sagittal Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 41642 / % possible obs: 91.03 % / Redundancy: 4.8 % / Biso Wilson estimate: 11.828 Å2 / Rsym value: 0.12 / Net I/σ(I): 9.8
Reflection shellResolution: 2→2.1 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.163 / Mean I/σ(I) obs: 8 / Num. unique all: 2432 / Rsym value: 0.24 / % possible all: 83.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ULD

1uld


Resolution: 2→14.84 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.935 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.135
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.24949 2260 5.2 %RANDOM
Rwork0.24267 ---
obs0.24301 41187 97.1 %-
all-41187 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.148 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.01 Å20 Å2
2--0.03 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2→14.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2626 0 0 238 2864
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222684
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.983636
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.2055324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.33623.582134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.87415462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3481524
X-RAY DIFFRACTIONr_chiral_restr0.4550.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022068
X-RAY DIFFRACTIONr_nbd_refined0.2370.31049
X-RAY DIFFRACTIONr_nbtor_refined0.3340.51801
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.5324
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3860.340
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.513
X-RAY DIFFRACTIONr_mcbond_it2.17621626
X-RAY DIFFRACTIONr_mcangle_it3.25632656
X-RAY DIFFRACTIONr_scbond_it2.32921058
X-RAY DIFFRACTIONr_scangle_it3.7463980
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1312 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.45
loose thermal3.4910
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 150 -
Rwork0.406 2836 -
obs--93.37 %

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