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- PDB-4tqj: Structural basis of specific recognition of non-reducing terminal... -

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Basic information

Entry
Database: PDB / ID: 4tqj
TitleStructural basis of specific recognition of non-reducing terminal N-acetylglucosamine by an Agrocybe aegerita lection
ComponentsLectin 2
KeywordsSUGAR BINDING PROTEIN / complex / lectin / GlcNAc
Function / homologyFG-GAP-like repeat / FG-GAP repeat / Integrin alpha, N-terminal / Lectin 2
Function and homology information
Biological speciesAgrocybe aegerita (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHu, Y.L. / Ren, X.M. / Li, D.F. / Jiang, S. / Lan, X.Q. / Sun, H. / Wang, D.C.
CitationJournal: Plos One / Year: 2015
Title: Structural Basis of Specific Recognition of Non-Reducing Terminal N-Acetylglucosamine by an Agrocybe aegerita Lectin.
Authors: Ren, X.M. / Li, D.F. / Jiang, S. / Lan, X.Q. / Hu, Y. / Sun, H. / Wang, D.C.
History
DepositionJun 11, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lectin 2
B: Lectin 2


Theoretical massNumber of molelcules
Total (without water)86,1652
Polymers86,1652
Non-polymers00
Water14,556808
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-6 kcal/mol
Surface area29240 Å2
Unit cell
Length a, b, c (Å)52.600, 111.700, 135.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lectin 2


Mass: 43082.289 Da / Num. of mol.: 2 / Mutation: I126T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrocybe aegerita (fungus) / Gene: aal-2 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: H6CS64
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 808 / Source method: isolated from a natural source / Formula: H2O

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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: 2.34 Å3/Da / Density % sol: 47.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 30% PEG 8000 (w/v), 0.2M sodium acetate and 0.1M sodium cacodylate pH 6.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54187 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jan 1, 2012 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2→86.31 Å / Num. all: 52439 / Num. obs: 52439 / % possible obs: 95.7 % / Redundancy: 5 % / Rpim(I) all: 0.027 / Rrim(I) all: 0.064 / Rsym value: 0.057 / Net I/av σ(I): 8.386 / Net I/σ(I): 16.8 / Num. measured all: 262862
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2-2.1130.2762.62030368820.1810.2763.887.9
2.11-2.244.50.2223.33148769820.1130.2226.494.1
2.24-2.395.20.1634.43442966790.0770.1638.894.6
2.39-2.585.10.1225.93163662120.0580.12210.895.2
2.58-2.8350.097.82978559130.0420.0914.297.6
2.83-3.165.10.06610.32786254510.0310.06619.498.7
3.16-3.655.50.04414.52683848860.020.04429.199.5
3.65-4.476.10.03419.22576741950.0150.03438.4100
4.47-6.326.80.03517.12244232990.0140.03537.5100
6.32-49.0576.30.0295.51231319400.0140.02935.199.8

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Processing

Software
NameVersionClassification
iMOSFLM3.3.9data reduction
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.7_650)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→49.057 Å / FOM work R set: 0.8475 / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2349 2596 5.05 %
Rwork0.1871 48791 -
obs0.1895 51387 93.44 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.208 Å2 / ksol: 0.338 e/Å3
Displacement parametersBiso max: 56.48 Å2 / Biso mean: 21.95 Å2 / Biso min: 2.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.6486 Å2-0 Å20 Å2
2---3.773 Å2-0 Å2
3---3.1243 Å2
Refinement stepCycle: final / Resolution: 2→49.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6034 0 0 808 6842
Biso mean---27.3 -
Num. residues----806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076172
X-RAY DIFFRACTIONf_angle_d1.058360
X-RAY DIFFRACTIONf_chiral_restr0.074892
X-RAY DIFFRACTIONf_plane_restr0.0041110
X-RAY DIFFRACTIONf_dihedral_angle_d12.8782122
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.03640.2986990.23862078217777
2.0364-2.07550.27471120.20912236234883
2.0755-2.11790.27261190.1992374249387
2.1179-2.1640.26281460.19162431257790
2.164-2.21430.22731200.18572462258291
2.2143-2.26970.23741460.18322466261291
2.2697-2.3310.26151350.18652511264692
2.331-2.39960.24841520.18392478263092
2.3996-2.47710.23431330.19622518265192
2.4771-2.56560.27111330.19622568270194
2.5656-2.66830.25451390.19992601274095
2.6683-2.78980.29131370.19622638277596
2.7898-2.93680.25041390.19992689282897
2.9368-3.12080.2611490.1952671282098
3.1208-3.36170.20741390.18872722286199
3.3617-3.69990.21061460.173827562902100
3.6999-4.2350.1931400.15727982938100
4.235-5.33470.20221480.15328452993100
5.3347-49.07190.24121640.231329493113100

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