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- PDB-2zgk: Crystal structure of wildtype AAL -

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Basic information

Entry
Database: PDB / ID: 2zgk
TitleCrystal structure of wildtype AAL
ComponentsAnti-tumor lectin
KeywordsHYDROLASE / galectin / jelly roll / Apoptosis / 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 / SIRAS / Resolution: 3 Å
AuthorsYang, N. / Li, D.F. / Wang, D.C.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural basis for the tumor cell apoptosis-inducing activity of an antitumor lectin from the edible mushroom Agrocybe aegerita
Authors: Yang, N. / Li, D.F. / Feng, L. / Xiang, Y. / Liu, W. / Sun, H. / Wang, D.C.
History
DepositionJan 23, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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


Theoretical massNumber of molelcules
Total (without water)16,9781
Polymers16,9781
Non-polymers00
Water00
1
A: Anti-tumor lectin

A: Anti-tumor lectin


Theoretical massNumber of molelcules
Total (without water)33,9562
Polymers33,9562
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area1730 Å2
ΔGint-11 kcal/mol
Surface area12470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.040, 124.040, 56.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Anti-tumor lectin / AAL


Mass: 16977.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Agrocybe aegerita (fungus) / Tissue: fruiting body
References: UniProt: Q6WY08, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters
Sequence detailsTHIS SEQUENCE IS ALLELE OF UNP Q6WY08.

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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: 3.71 Å3/Da / Density % sol: 66.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 5% glycerol, 1.7M ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 5791 / Num. obs: 5762 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8 % / Biso Wilson estimate: 44 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.065 / Net I/σ(I): 22.4
Reflection shellResolution: 3→3.12 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 11.7 / Num. unique all: 543 / Rsym value: 0.298 / % possible all: 99

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Processing

Software
NameVersionClassification
CrystalCleardata collection
SHARPphasing
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 3→41.85 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.283 573 -random
Rwork0.253 ---
obs0.282 5400 98.2 %-
all-5498 --
Displacement parametersBiso mean: 53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.77 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 3→41.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1199 0 0 0 1199
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.51
LS refinement shellResolution: 3→3.11 Å / Rfactor Rfree error: 0.039
RfactorNum. reflection% reflection
Rfree0.42 54 -
Rwork0.34 --
obs-463 98 %

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