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- PDB-1ww5: Agrocybe cylindracea galectin complexed with 3'-sulfonyl lactose -

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Basic information

Entry
Database: PDB / ID: 1ww5
TitleAgrocybe cylindracea galectin complexed with 3'-sulfonyl lactose
Componentsgalectin
KeywordsSUGAR BINDING PROTEIN / Agrocybe cylindracea galectin / fungal galectin / carbohydrate recognition domain / 3'-sulfated lactose / X-ray crystallographic analysis
Function / homology
Function and homology information


DNA nuclease activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / polysaccharide binding / positive regulation of apoptotic process / apoptotic process
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
lactose-3'-sulfate / Anti-tumor lectin
Similarity search - Component
Biological speciesAgrocybe cylindracea (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBan, M. / Yoon, H.J. / Demirkan, E. / Utsumi, S. / Mikami, B. / Yagi, F.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Structural Basis of a Fungal Galectin from Agrocybe cylindracea for Recognizing Sialoconjugate
Authors: Ban, M. / Yoon, H.J. / Demirkan, E. / Utsumi, S. / Mikami, B. / Yagi, F.
History
DepositionJan 3, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 23, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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: galectin
B: galectin
C: galectin
D: galectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3248
Polymers67,6354
Non-polymers1,6894
Water6,521362
1
A: galectin
D: galectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6624
Polymers33,8172
Non-polymers8452
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-1 kcal/mol
Surface area13010 Å2
MethodPISA
2
B: galectin
C: galectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6624
Polymers33,8172
Non-polymers8452
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-1 kcal/mol
Surface area13010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.623, 57.648, 64.643
Angle α, β, γ (deg.)89.96, 111.65, 90.14
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
galectin


Mass: 16908.744 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Agrocybe cylindracea (fungus) / References: UniProt: Q6WY08*PLUS
#2: Polysaccharide
3-O-sulfo-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / lactose-3'-sulfate


Type: oligosaccharide, Oligosaccharide / Class: Glycan component / Mass: 422.360 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: lactose-3'-sulfate
DescriptorTypeProgram
DGalp[3S]b1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5_3*OSO/3=O/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp3SO3]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 2.4 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: ammomium sulfate, lactose, pipes, 3'-sulfonyl lactose, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Aug 22, 2001 / Details: carbon monochromater
RadiationMonochromator: carbon monochromater / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30.7 Å / Num. all: 32857 / Num. obs: 31157 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 2.71 % / Biso Wilson estimate: 14.8 Å2 / Rsym value: 0.033 / Net I/σ(I): 28.04
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 1.32 % / Mean I/σ(I) obs: 5.83 / Num. unique all: 2998 / Rsym value: 0.143 / % possible all: 93

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Processing

Software
NameVersionClassification
CNS1refinement
SADIEdata reduction
SAINTdata reduction
SAINTdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→10 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 822170.94 / 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
Rfree0.267 2978 10 %RANDOM
Rwork0.198 ---
obs0.198 29778 92.6 %-
all-32103 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.9049 Å2 / ksol: 0.328932 e/Å3
Displacement parametersBiso mean: 33.8 Å2
Baniso -1Baniso -2Baniso -3
1-8.04 Å21.62 Å2-1.27 Å2
2---1.48 Å20 Å2
3----6.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4772 0 108 362 5242
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d27.6
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_mcbond_it7.351.5
X-RAY DIFFRACTIONc_mcangle_it8.952
X-RAY DIFFRACTIONc_scbond_it10.22
X-RAY DIFFRACTIONc_scangle_it11.492.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.372 459 10.4 %
Rwork0.308 3959 -
obs--82.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION3ION.PARAMWATER.TOP
X-RAY DIFFRACTION4PARAM3.CHOTOPH3.CHO

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