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

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Basic information

Entry
Database: PDB / ID: 4tqk
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 / SYNCHROTRON / Resolution: 2.1 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 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_radiation_wavelength ...chem_comp / diffrn_radiation_wavelength / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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: Lectin 2
B: Lectin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,59813
Polymers86,1652
Non-polymers2,43311
Water15,745874
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint30 kcal/mol
Surface area28700 Å2
Unit cell
Length a, b, c (Å)52.560, 111.240, 134.630
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: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 874 / 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: 2.3 Å3/Da / Density % sol: 46.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 25% PEG 4000 (w/v), 6% Tacsimate pH 6.0 and 0.1M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jan 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→85.754 Å / Num. all: 41489 / Num. obs: 41489 / % possible obs: 88.8 % / Redundancy: 3 % / Rpim(I) all: 0.085 / Rrim(I) all: 0.166 / Rsym value: 0.141 / Net I/av σ(I): 5.185 / Net I/σ(I): 6.3 / Num. measured all: 126025
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
2.1-2.211.80.411.9846846840.320.412.270.4
2.21-2.351.90.3592.1969149950.2740.3592.578.6
2.35-2.512.10.3162.41088751650.240.3162.986.1
2.51-2.712.40.2772.81228251130.1990.2773.592.1
2.71-2.972.90.2143.61397949000.140.214595.1
2.97-3.323.40.164.71552945600.0940.167.296.8
3.32-3.8340.1126.71664041400.0620.1121198.9
3.83-4.74.60.0937.91623835490.0480.09313.699.4
4.7-6.6450.116.51410528160.0540.1111.599.8
6.64-26.285.20.0897.3820615670.0420.08913.896.1

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.7_650)refinement
SCALAdata scaling
RefinementResolution: 2.1→26.28 Å / FOM work R set: 0.8568 / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2408 1974 4.98 %
Rwork0.1714 37671 -
obs0.1748 39645 84.54 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.619 Å2 / ksol: 0.371 e/Å3
Displacement parametersBiso max: 61.18 Å2 / Biso mean: 12.39 Å2 / Biso min: 2.17 Å2
Baniso -1Baniso -2Baniso -3
1--2.2351 Å20 Å20 Å2
2--1.3548 Å2-0 Å2
3---0.8803 Å2
Refinement stepCycle: final / Resolution: 2.1→26.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6034 0 165 874 7073
Biso mean--15.08 19.23 -
Num. residues----806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076337
X-RAY DIFFRACTIONf_angle_d1.0938591
X-RAY DIFFRACTIONf_chiral_restr0.07947
X-RAY DIFFRACTIONf_plane_restr0.0041121
X-RAY DIFFRACTIONf_dihedral_angle_d14.8852210
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.15250.36871120.23321843195560
2.1525-2.21070.32281110.2152050216165
2.2107-2.27570.25491200.2062188230870
2.2757-2.34910.26971180.20832282240073
2.3491-2.4330.33071020.20062462256477
2.433-2.53030.33481400.20552577271781
2.5303-2.64540.26741530.19282692284586
2.6454-2.78470.28331470.1872826297390
2.7847-2.9590.26771770.18112885306292
2.959-3.18710.21391280.17123017314594
3.1871-3.50710.21421480.15473147329597
3.5071-4.01310.19031630.12863157332098
4.0131-5.05020.16271610.11853213337499
5.0502-26.2820.21011940.18423332352698

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