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- PDB-1ww7: Agrocybe cylindracea galectin (Ligand-free) -

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Basic information

Entry
Database: PDB / ID: 1ww7
TitleAgrocybe cylindracea galectin (Ligand-free)
Componentsgalectin
KeywordsSUGAR BINDING PROTEIN / Agrocybe cylindracea galectin / fungal galectin / carbohydrate recognition domain / X-ray crystallographic analysis / sulfate ion
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
Biological speciesAgrocybe cylindracea (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)68,0198
Polymers67,6354
Non-polymers3844
Water8,161453
1
A: galectin
D: galectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9143
Polymers33,8172
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-37 kcal/mol
Surface area13130 Å2
MethodPISA
2
B: galectin
C: galectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1065
Polymers33,8172
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-42 kcal/mol
Surface area13170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.071, 96.307, 121.656
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 453 / 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: 2.4 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: ammomium sulfate, pipes, 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: Feb 10, 1999 / 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: 1.9→41.7 Å / Num. all: 53735 / Num. obs: 51284 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 5.32 % / Biso Wilson estimate: 1.3 Å2 / Rsym value: 0.109 / Net I/σ(I): 11.09
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.95 % / Mean I/σ(I) obs: 1.86 / Num. unique all: 4562 / Rsym value: 0.464 / % possible all: 85.9

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Processing

Software
NameVersionClassification
CNS1refinement
SADIEdata reduction
SAINTdata reduction
SAINTdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→10 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 503729.2 / 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
Rfree0.252 4576 10.1 %RANDOM
Rwork0.203 ---
obs0.203 45357 85.2 %-
all-53183 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 77.9027 Å2 / ksol: 0.367265 e/Å3
Displacement parametersBiso mean: 18 Å2
Baniso -1Baniso -2Baniso -3
1-2.88 Å20 Å20 Å2
2---1.35 Å20 Å2
3----1.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4803 0 20 453 5276
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d27.6
X-RAY DIFFRACTIONc_improper_angle_d0.66
X-RAY DIFFRACTIONc_mcbond_it4.591.5
X-RAY DIFFRACTIONc_mcangle_it5.482
X-RAY DIFFRACTIONc_scbond_it6.792
X-RAY DIFFRACTIONc_scangle_it8.532.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.344 633 10.3 %
Rwork0.318 5529 -
obs--70.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMCARBOHYDRATE.TOP

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