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- PDB-3wg2: Crystal structure of Agrocybe cylindracea galectin mutant (N46A) -

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Basic information

Entry
Database: PDB / ID: 3wg2
TitleCrystal structure of Agrocybe cylindracea galectin mutant (N46A)
ComponentsGalactoside-binding lectin
KeywordsSUGAR BINDING PROTEIN / galectin / galactose binding
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
TRIETHYLENE GLYCOL / Anti-tumor lectin
Similarity search - Component
Biological speciesAgrocybe aegerita (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKuwabara, N. / Hu, D. / Tateno, H. / Makio, H. / Hirabayashi, J. / Kato, R.
CitationJournal: Febs Lett. / Year: 2013
Title: Conformational change of a unique sequence in a fungal galectin from Agrocybe cylindracea controls glycan ligand-binding specificity.
Authors: Kuwabara, N. / Hu, D. / Tateno, H. / Makyio, H. / Hirabayashi, J. / Kato, R.
History
DepositionJul 25, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.2Nov 8, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / 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: Galactoside-binding lectin
B: Galactoside-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0723
Polymers37,9222
Non-polymers1501
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-4 kcal/mol
Surface area12590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.925, 124.925, 56.967
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Galactoside-binding lectin


Mass: 18961.080 Da / Num. of mol.: 2 / Mutation: N46A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrocybe aegerita (fungus) / Plasmid: pET27b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6WY08*PLUS
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THE AUTHOR STATES THERE IS MUTATION N46A.

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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: 3.38 Å3/Da / Density % sol: 63.65 % / Mosaicity: 0.324 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 30% PEG 4000, 0.2M ammonium acetate, 0.1M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→35 Å / Num. obs: 25947 / % possible obs: 99.8 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.076 / Χ2: 1.789 / Net I/σ(I): 12
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.2811.20.4325901.5031100
2.28-2.3711.20.39825711.4971100
2.37-2.4811.30.27325681.4991100
2.48-2.6111.30.22925811.4661100
2.61-2.7711.30.16225871.5141100
2.77-2.9911.30.12225971.5741100
2.99-3.2911.30.07825941.751100
3.29-3.7611.30.05926011.9981100
3.76-4.7411.20.05126172.2251100
4.74-3510.70.05826412.899198.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1WW7

1ww7


Resolution: 2.2→27.39 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0 / SU B: 9.376 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2443 1307 5 %RANDOM
Rwork0.2111 ---
obs0.2127 25919 99.75 %-
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 max: 111.93 Å2 / Biso mean: 53.4639 Å2 / Biso min: 29.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.2→27.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2292 0 10 106 2408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022340
X-RAY DIFFRACTIONr_angle_refined_deg1.0671.9353191
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3155304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.25325.41796
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26315361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.874156
X-RAY DIFFRACTIONr_chiral_restr0.0660.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021736
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 100 -
Rwork0.278 1724 -
all-1824 -
obs--99.78 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.5885-0.8271-0.02811.8938-0.17791.0014-0.1355-0.0218-0.06890.0740.0808-0.20880.10820.01170.05470.06620.02980.01330.0312-0.01630.0537.705238.11612.3419
22.9107-0.81460.03662.01370.0560.64640.00270.1120.16430.0922-0.04710.16570.0557-0.09850.04440.0179-0.00270.02290.0992-0.00230.04614.103851.7576-2.2661
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 161
2X-RAY DIFFRACTION2B3 - 161

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