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

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Basic information

Entry
Database: PDB / ID: 3kif
TitleThe crystal structures of two fragments truncated from 5-bladed beta-propeller lectin, tachylectin-2 (Lib1-B7-18 and Lib2-D2-15)
Components5-bladed beta-propeller lectin
KeywordsSUGAR BINDING PROTEIN / 5-bladed -propeller / Structural Genomics / Israel Structural Proteomics Center / ISPC
Function / homology
Function and homology information


carbohydrate binding / innate immune response / extracellular region
Similarity search - Function
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 / SYNCHROTRON / Resolution: 2.5 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 2.1Mar 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

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
F: 5-bladed beta-propeller lectin
G: 5-bladed beta-propeller lectin
H: 5-bladed beta-propeller lectin
I: 5-bladed beta-propeller lectin
J: 5-bladed beta-propeller lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,61821
Polymers120,45310
Non-polymers2,16511
Water88349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
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)61,41811
Polymers60,2265
Non-polymers1,1926
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13000 Å2
ΔGint-93 kcal/mol
Surface area20010 Å2
MethodPISA
3
F: 5-bladed beta-propeller lectin
G: 5-bladed beta-propeller lectin
H: 5-bladed beta-propeller lectin
I: 5-bladed beta-propeller lectin
J: 5-bladed beta-propeller lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,19910
Polymers60,2265
Non-polymers9735
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13240 Å2
ΔGint-94 kcal/mol
Surface area19830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.558, 80.558, 170.681
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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


Mass: 12045.268 Da / Num. of mol.: 10 / Fragment: residues 1-106
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / 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.: 9 / Source method: obtained synthetically / Formula: C8H13NO6
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.65 Å3/Da / Density % sol: 53.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.5
Details: 100mM Bis-Tris, 0.2M lithium chloride, 19% PEG 3350, pH 5.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 27, 2008
RadiationMonochromator: channel cut ESRF monochromator and a new torodial focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 42804 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.118 / Rsym value: 0.114 / Net I/σ(I): 34.6
Reflection shellResolution: 2.5→2.544 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 4.2 / Num. unique all: 2111 / % possible all: 98.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementResolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.887 / SU B: 9.277 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.456 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27613 2145 5 %RANDOM
Rwork0.2131 ---
obs0.21625 40432 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.867 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å2-0.45 Å20 Å2
2---0.9 Å20 Å2
3---1.35 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7336 0 145 49 7530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0227749
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.421.92810518
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7475892
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.49323.333411
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.49151050
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4071538
X-RAY DIFFRACTIONr_chiral_restr0.1720.2966
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026329
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2520.23237
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3360.25180
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2226
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2580.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2270.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3261.54580
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.16627086
X-RAY DIFFRACTIONr_scbond_it3.29833848
X-RAY DIFFRACTIONr_scangle_it4.5984.53432
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.498→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.467 161 -
Rwork0.337 2891 -
obs--95.7 %

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