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- PDB-3m3q: Crystal Structure of Agrocybe aegerita lectin AAL complexed with ... -

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Basic information

Entry
Database: PDB / ID: 3m3q
TitleCrystal Structure of Agrocybe aegerita lectin AAL complexed with Ganglosides GM1 pentasaccharide
ComponentsAnti-tumor lectin
KeywordsHYDROLASE / galectin / AAL / Ganglosides GM1 / Apoptosis / Lectin / Nuclease
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 aegerita (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFeng, L. / Li, D. / Wang, D.
CitationJournal: Faseb J. / Year: 2010
Title: Structural insights into the recognition mechanism between an antitumor galectin AAL and the Thomsen-Friedenreich antigen
Authors: Feng, L. / Sun, H. / Zhang, Y. / Li, D.F. / Wang, D.C.
History
DepositionMar 9, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / 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.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Anti-tumor lectin
B: Anti-tumor lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2164
Polymers34,2182
Non-polymers1,9982
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-14 kcal/mol
Surface area12770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.861, 66.711, 56.211
Angle α, β, γ (deg.)90.000, 93.180, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Anti-tumor lectin / AAL


Mass: 17108.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrocybe aegerita (fungus) / Gene: AAL / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q6WY08, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters
#2: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha- ...beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 998.885 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGalpNAcb1-4[DNeup5Aca2-3]DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a2112h-1b_1-5_2*NCC/3=O]/1-2-3-4-2/a4-b1_b3-c2_b4-d1_d3-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}[(4+1)][b-D-GalpNAc]{[(3+1)][b-D-Galp]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsIT IS AN ALLELE GENE OF THE GENE IN THE GENBANK DATABASE.

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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: 2.78 Å3/Da / Density % sol: 55.8 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 5.5
Details: 25% PEG3350, 0.2M LiCl, 5% acetone, pH 5.5, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. all: 19640 / Num. obs: 19388 / % possible obs: 98.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.123 / Rsym value: 0.123 / Χ2: 6.674 / Net I/σ(I): 13.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.18-2.2230.2349333.27595
2.22-2.263.40.2219463.02497.5
2.26-2.33.40.2239843.11898.6
2.3-2.353.60.2149393.63199.4
2.35-2.43.60.2129644.14899.3
2.4-2.463.70.1899784.07999.7
2.46-2.523.70.199813.70999.8
2.52-2.583.70.1779664.57899.8
2.58-2.663.70.1639935.035100
2.66-2.753.70.1589525.88899.9
2.75-2.843.70.159906.207100
2.84-2.963.70.1399786.79199.9
2.96-3.093.70.1329757.70199.7
3.09-3.263.70.1229648.75299.5
3.26-3.463.70.1159699.60598.8
3.46-3.733.60.11598411.33898.9
3.73-4.13.60.11197210.86398.4
4.1-4.73.50.10995411.92295.9
4.7-5.913.60.0989659.33697.3
5.91-503.50.09210019.2597.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZGL

2zgl


Resolution: 2.2→50 Å / FOM work R set: 0.835 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 925 4.8 %RANDOM
Rwork0.209 ---
all0.222 19640 --
obs0.222 18981 98.8 %-
Solvent computationBsol: 42.882 Å2
Displacement parametersBiso mean: 28.016 Å2
Baniso -1Baniso -2Baniso -3
1-10.607 Å20 Å25.116 Å2
2--0.599 Å20 Å2
3----11.206 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2412 0 136 165 2713
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.404
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2-2.240.285500.2199751025
2.24-2.290.299590.239901049
2.29-2.340.27530.22410031056
2.34-2.390.264460.2329911037
2.39-2.450.276530.21710081061
2.45-2.520.266480.23510031051
2.52-2.590.285400.21410201060
2.59-2.680.275640.2210091073
2.68-2.770.215500.19210111061
2.77-2.880.31470.25210061053
2.88-3.010.314450.23110241069
3.01-3.170.237440.23210141058
3.17-3.370.273610.22610071068
3.37-3.630.232540.2199931047
3.63-40.236590.2069921051
4-4.580.212470.1589911038
4.58-5.760.21470.1689991046
5.76-500.223580.21610201078
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2gm1.param
X-RAY DIFFRACTION3water_rep.param

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