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- PDB-3kih: The crystal structures of two fragments truncated from 5-bladed b... -

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Basic information

Entry
Database: PDB / ID: 3kih
TitleThe crystal structures of two fragments truncated from 5-bladed beta-propeller lectin, tachylectin-2 (Lib2-D2-15)
Components5-bladed beta-propeller lectin
KeywordsSUGAR BINDING PROTEIN / 5-bladed beta-propeller / Structural Genomics / Israel Structural Proteomics Center / ISPC
Function / homology
Function and homology information


carbohydrate binding / innate immune response / extracellular region
Similarity search - Function
N-terminal domain of TfIIb - #510 / Tachylectin-2-like / Tachylectin 2 / Tachylectin 2 superfamily / Tachylectin / N-terminal domain of TfIIb / Single Sheet / Mainly Beta
Similarity search - Domain/homology
2-(acetylamido)-2-deoxy-D-glucono-1,5-lactone / Tachylectin-2
Similarity search - Component
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsDym, O. / Tawfik, D.S. / Yadid, I. / Israel Structural Proteomics Center (ISPC)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Metamorphic proteins mediate evolutionary transitions of structure
Authors: Yadid, I. / Kirshenbaum, N. / Sharon, M. / Dym, O. / Tawfik, D.S.
History
DepositionNov 2, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2014Group: Database references
Revision 1.3Mar 19, 2014Group: Source and taxonomy / Structure summary
Revision 2.0Jul 29, 2020Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5-bladed beta-propeller lectin
B: 5-bladed beta-propeller lectin
C: 5-bladed beta-propeller lectin
D: 5-bladed beta-propeller lectin
E: 5-bladed beta-propeller lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9679
Polymers54,0905
Non-polymers8774
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10110 Å2
ΔGint-65 kcal/mol
Surface area20760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.566, 56.418, 86.306
Angle α, β, γ (deg.)90.00, 122.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
5-bladed beta-propeller lectin / tachylectin-2


Mass: 10818.021 Da / Num. of mol.: 5 / Fragment: residues 1-97
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pETtr / Production host: Escherichia coli (E. coli) / References: UniProt: Q27084*PLUS
#2: Sugar
ChemComp-GDL / 2-(acetylamido)-2-deoxy-D-glucono-1,5-lactone / 2-ACETAMIDO-2-DEOXY-D-GLUCONO-1,5-LACTONE


Type: D-saccharide / Mass: 219.192 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H13NO6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 2.37 Å3/Da / Density % sol: 48.16 %
Crystal growTemperature: 298 K / Method: microbatch under oil / pH: 7
Details: 100mM HEPES, 0.2M magnesium chloride, 20% PEG 6000, pH 7, Microbatch under oil, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 6, 2009
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 17718 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.5→2.54 Å / % possible all: 90.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TL2

1tl2


Resolution: 2.49→50 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.877 / SU B: 12.608 / SU ML: 0.277 / Cross valid method: THROUGHOUT / ESU R: 0.846 / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29903 905 5.1 %RANDOM
Rwork0.23311 ---
obs0.23654 16813 98.43 %-
all-17081 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.346 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å2-2.01 Å2
2--0.04 Å20 Å2
3----1.75 Å2
Refinement stepCycle: LAST / Resolution: 2.49→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3675 0 60 6 3741
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223868
X-RAY DIFFRACTIONr_angle_refined_deg1.521.9525252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0075449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.09624.444189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.73715565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3721510
X-RAY DIFFRACTIONr_chiral_restr0.1070.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213073
X-RAY DIFFRACTIONr_mcbond_it0.561.52263
X-RAY DIFFRACTIONr_mcangle_it1.05223607
X-RAY DIFFRACTIONr_scbond_it1.34631605
X-RAY DIFFRACTIONr_scangle_it2.1624.51645
LS refinement shellResolution: 2.49→2.555 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.512 51 -
Rwork0.351 1106 -
obs--85.51 %

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