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- PDB-1ul9: CGL2 ligandfree -

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Basic information

Entry
Database: PDB / ID: 1ul9
TitleCGL2 ligandfree
Componentsgalectin-2
KeywordsSUGAR BINDING PROTEIN / galectin / lectin / beta-galactoside binding lectin / sugar binding
Function / homology
Function and homology information


endomembrane system / carbohydrate binding / extracellular region / membrane
Similarity search - Function
Galectin / 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 speciesCoprinopsis cinerea (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsWalser, P.J. / Haebel, P.W. / Kuenzler, M. / Kues, U. / Aebi, M. / Ban, N.
Citation
Journal: STRUCTURE / Year: 2004
Title: Structure and Functional Analysis of the Fungal Galectin CGL2
Authors: Walser, P.J. / Haebel, P.W. / Kuenzler, M. / Sargent, D. / Kues, U. / Aebi, M. / Ban, N.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 1998
Title: Crystallography & NMR system: A new software suite for macromolecular structure determination.
Authors: Brunger, A.T. / Adams, P.D. / Clore, G.M. / DeLano, W.L. / Gros, P. / Grosse-Kunstleve, R.W. / Jiang, J.S. / Kuszewski, J. / Nilges, M. / Pannu, N.S. / Read, R.J. / Rice, L.M. / Simonson, T. / Warren, G.L.
History
DepositionSep 12, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: galectin-2
B: galectin-2


Theoretical massNumber of molelcules
Total (without water)33,5342
Polymers33,5342
Non-polymers00
Water5,459303
1
A: galectin-2
B: galectin-2

A: galectin-2
B: galectin-2


Theoretical massNumber of molelcules
Total (without water)67,0684
Polymers67,0684
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area7300 Å2
ΔGint-20 kcal/mol
Surface area24530 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)67.878, 114.615, 49.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Detailsgalectin tetramer from crystallographic dimer by -x -y, z

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Components

#1: Protein galectin-2 / CGL2


Mass: 16766.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coprinopsis cinerea (fungus) / Gene: cgl2 / Plasmid: pYADE4 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): SEY 6210 / References: UniProt: Q9P4R8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.57 Å3/Da / Density % sol: 51.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: PEG 3350, PEG 400, sodium phosphate, sodium chloride, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 8, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.22→43.79 Å / Num. all: 19215 / Num. obs: 19215 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 18.3 Å2 / Limit h max: 30 / Limit h min: 0 / Limit k max: 51 / Limit k min: 0 / Limit l max: 22 / Limit l min: 0 / Observed criterion F max: 1362778.32 / Observed criterion F min: 2.35 / Rsym value: 0.068 / Net I/σ(I): 21.8
Reflection shellResolution: 2.22→2.32 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 9.8 / Num. unique all: 1334 / Rsym value: 0.141 / % possible all: 66.8

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CGL2-lactose

Resolution: 2.22→43.79 Å / Rfactor Rfree error: 0.008 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.256 935 4.9 %random
Rwork0.202 ---
all-19189 --
obs-19189 96.5 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 46.2926 Å2 / ksol: 0.371495 e/Å3
Displacement parametersBiso max: 75.58 Å2 / Biso mean: 21.2 Å2 / Biso min: 7.25 Å2
Baniso -1Baniso -2Baniso -3
1-3.13 Å20 Å20 Å2
2---6.57 Å20 Å2
3---3.44 Å2
Refine Biso
ClassRefine-IDTreatment
polymerX-RAY DIFFRACTIONisotropic
waterX-RAY DIFFRACTIONisotropic
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.09 Å
Luzzati d res high-2.22
Refinement stepCycle: LAST / Resolution: 2.22→43.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2376 0 0 303 2679
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_torsion_deg26.5
X-RAY DIFFRACTIONc_torsion_impr_deg0.75
X-RAY DIFFRACTIONc_mcbond_it1.181.5
X-RAY DIFFRACTIONc_mcangle_it1.762
X-RAY DIFFRACTIONc_scbond_it1.952
X-RAY DIFFRACTIONc_scangle_it2.72.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.22-2.320.25710750.20120240.0252431213187.6
2.32-2.440.2811074.70.20321900.0272465229793.2
2.44-2.590.2711084.60.19722200.0262432232895.7
2.59-2.790.2781134.60.20723180.0262472243198.3
2.79-3.070.2531214.90.20723240.0232469244599
3.07-3.520.2441295.30.20923280.0212481245799
3.52-4.430.2511174.70.19323880.0232522250599.3
4.43-43.790.251335.10.20224620.0222640259598.3
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2carbohydrate.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5cis_peptide.param

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