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- PDB-3m3o: Crystal Structure of Agrocybe aegerita lectin AAL mutant R85A com... -

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Basic information

Entry
Database: PDB / ID: 3m3o
TitleCrystal Structure of Agrocybe aegerita lectin AAL mutant R85A complexed with p-Nitrophenyl TF disaccharide
ComponentsAnti-tumor lectin
KeywordsHYDROLASE / galectin / AAL / muitant / Thomsen-Friedenreich antigen / Apoptosis / Lectin / Nuclease / GAL-BETA-1 / 3-GALNAC-ALPHA-O-P-Nitrophenyl
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
Thomsen-Friedenreich antigen / P-NITROPHENOL / Anti-tumor lectin
Similarity search - Component
Biological speciesAgrocybe aegerita (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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 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 / 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_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_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

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Assembly

Deposited unit
A: Anti-tumor lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6234
Polymers16,8921
Non-polymers7323
Water99155
1
A: Anti-tumor lectin
hetero molecules

A: Anti-tumor lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2478
Polymers33,7832
Non-polymers1,4636
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area1760 Å2
ΔGint-12 kcal/mol
Surface area12620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.560, 42.560, 125.300
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Anti-tumor lectin / AAL


Mass: 16891.684 Da / Num. of mol.: 1 / Mutation: R85A
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-alpha-D-galactopyranose / Thomsen-Friedenreich antigen


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: Thomsen-Friedenreich antigen
DescriptorTypeProgram
DGalpb1-3DGalpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GalpNAc]{[(3+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-NPO / P-NITROPHENOL


Mass: 139.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO3
#4: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 1.94 Å3/Da / Density % sol: 36.58 %
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: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→36.893 Å / Num. all: 8217 / Num. obs: 8216 / % possible obs: 100 % / Redundancy: 5.9 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 10.4
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 5.7 / Num. unique all: 1183 / Rsym value: 0.279 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALAdata processing
CNSrefinement
PDB_EXTRACT3.004data extraction
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZGL

2zgl


Resolution: 2.1→36.86 Å / FOM work R set: 0.803 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 446 5.4 %RANDOM
Rwork0.217 ---
all0.235 8217 --
obs0.235 8216 100 %-
Solvent computationBsol: 47.237 Å2
Displacement parametersBiso mean: 37.242 Å2
Baniso -1Baniso -2Baniso -3
1-6.919 Å20 Å20 Å2
2--6.919 Å20 Å2
3----13.837 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.1→36.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1193 0 49 55 1297
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.427
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1-2.20.316490.24943992
2.2-2.310.308570.226939996
2.31-2.460.267530.2349521005
2.46-2.650.396590.259691028
2.65-2.910.333490.268950999
2.91-3.330.239490.2359721021
3.33-4.20.265670.1939841051
4.2-500.19630.19610611124
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2tfg.param
X-RAY DIFFRACTION3BTB.param
X-RAY DIFFRACTION4water_rep.param

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