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- PDB-1tl2: TACHYLECTIN-2 FROM TACHYPLEUS TRIDENTATUS (JAPANESE HORSESHOE CRAB) -

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Basic information

Entry
Database: PDB / ID: 1tl2
TitleTACHYLECTIN-2 FROM TACHYPLEUS TRIDENTATUS (JAPANESE HORSESHOE CRAB)
ComponentsPROTEIN (TACHYLECTIN-2)
KeywordsSUGAR BINDING PROTEIN / ANIMAL LECTIN / HORSESHOE CRAB / N-ACETYLGLUCOSAMINE / BETA-PROPELLER
Function / homology
Function and homology information


carbohydrate binding / innate immune response / extracellular region
Similarity search - Function
Tachylectin 2 / Tachylectin 2 / Tachylectin 2 superfamily / Tachylectin / 5 Propeller / Tachylectin-2; Chain A / Mainly Beta
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-glucopyranose / Tachylectin-2
Similarity search - Component
Biological speciesTachypleus tridentatus (Chinese horseshoe crab)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2 Å
AuthorsBeisel, H.-G. / Kawabata, S. / Iwanaga, S. / Huber, R. / Bode, W.
CitationJournal: EMBO J. / Year: 1999
Title: Tachylectin-2: crystal structure of a specific GlcNAc/GalNAc-binding lectin involved in the innate immunity host defense of the Japanese horseshoe crab Tachypleus tridentatus.
Authors: Beisel, H.G. / Kawabata, S. / Iwanaga, S. / Huber, R. / Bode, W.
History
DepositionDec 14, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 15, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
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 / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: 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: PROTEIN (TACHYLECTIN-2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9326
Polymers26,8261
Non-polymers1,1065
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.460, 89.460, 73.620
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein PROTEIN (TACHYLECTIN-2) / L10


Mass: 26825.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: FORMERLY NAMED L10, NOW TACHYLECTIN-2
Source: (natural) Tachypleus tridentatus (Chinese horseshoe crab)
References: UniProt: Q27084
#2: Sugar
ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE / N-Acetylglucosamine


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 3.14 Å3/Da / Density % sol: 61 %
Crystal growpH: 4.6 / Details: pH 4.6
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.1 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
210 mMMops1drop
35 mMGlcNAc1drop
4100 mMsodium acetate1reservoir
52.0 Msodium formate1reservoir

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→15.2 Å / Num. obs: 20896 / % possible obs: 93.7 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.074
Reflection shellResolution: 2.03→2.43 Å / Rmerge(I) obs: 0.171 / % possible all: 92.2
Reflection
*PLUS
Num. measured all: 83799
Reflection shell
*PLUS
% possible obs: 92.2 %

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Processing

Software
NameVersionClassification
CCP4model building
SHELXL-97model building
SHARPphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CCP4phasing
SHELXL-97phasing
RefinementMethod to determine structure: MIR / Resolution: 2→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.202 2072 10 %RANDOM
Rwork0.162 ---
obs-20892 94 %-
Displacement parametersBiso mean: 27.8 Å2
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1905 0 75 158 2138
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_angle_d0.025
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 18820
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.6

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