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- PDB-2zgl: Crystal structure of recombinant Agrocybe aegerita (rAAL) -

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Basic information

Entry
Database: PDB / ID: 2zgl
TitleCrystal structure of recombinant Agrocybe aegerita (rAAL)
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anti-tumor lectin
B: Anti-tumor lectin


Theoretical massNumber of molelcules
Total (without water)36,3602
Polymers36,3602
Non-polymers00
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-12 kcal/mol
Surface area13090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.200, 66.010, 57.860
Angle α, β, γ (deg.)90.00, 109.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Anti-tumor lectin / AAL


Mass: 18180.150 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / Source method: isolated from a natural source / Formula: H2O
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: 2.64 Å3/Da / Density % sol: 53.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 50mM Sodium Acetate, 5% PEG 1000, 5% PEG 8000, pH 4.6, 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: Apr 16, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→37.66 Å / Num. all: 31292 / Num. obs: 31292 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 13.2 Å2 / Rmerge(I) obs: 0.114 / Rsym value: 0.114 / Net I/σ(I): 9.6
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 5.9 / Num. unique all: 4557 / Rsym value: 0.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.2refinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZGK

2zgk


Resolution: 1.9→24.48 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1001699.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2984 10 %RANDOM
Rwork0.188 ---
obs0.188 29837 99.8 %-
all-31292 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.5994 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 20.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.45 Å20 Å26.49 Å2
2---1.44 Å20 Å2
3----1.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.9→24.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2428 0 0 401 2829
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d27.3
X-RAY DIFFRACTIONc_improper_angle_d0.68
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.291 483 9.8 %
Rwork0.242 4445 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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