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- PDB-2zx2: Rhamnose-binding lectin CSL3 -

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Basic information

Entry
Database: PDB / ID: 2zx2
TitleRhamnose-binding lectin CSL3
ComponentsCSL3
KeywordsIMMUNE SYSTEM / SUGAR BINDING PROTEIN / LECTIN / RHAMNOSE / INNATE IMMUNITY
Function / homology
Function and homology information


rhamnose binding / melibiose binding / cortical granule / galactose binding / NLS-dependent protein nuclear import complex / female germ cell nucleus / protein homodimerization activity / cytoplasm
Similarity search - Function
Rhamnose-binding lectin domain (RBL) / D-galactoside/L-rhamnose binding SUEL lectin domain superfamily / D-galactoside/L-rhamnose binding SUEL lectin domain / Galactose binding lectin domain / SUEL-type lectin domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / alpha-L-rhamnopyranose / L-rhamnose-binding lectin CSL3
Similarity search - Component
Biological speciesOncorhynchus keta (chum salmon)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsShirai, T. / Watababe, Y. / Lee, M. / Ogawa, T. / Muramoto, K.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structure of rhamnose-binding lectin CSL3: unique pseudo-tetrameric architecture of a pattern recognition protein
Authors: Shirai, T. / Watanabe, Y. / Lee, M.S. / Ogawa, T. / Muramoto, K.
History
DepositionDec 19, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 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

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Assembly

Deposited unit
A: CSL3
B: CSL3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9639
Polymers43,0912
Non-polymers8727
Water8,881493
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-35 kcal/mol
Surface area20070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.690, 75.376, 94.992
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CSL3


Mass: 21545.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oncorhynchus keta (chum salmon) / References: UniProt: P86179*PLUS
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Sugar ChemComp-RAM / alpha-L-rhamnopyranose / alpha-L-rhamnose / 6-deoxy-alpha-L-mannopyranose / L-rhamnose / rhamnose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LRhapaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-rhamnopyranoseCOMMON NAMEGMML 1.0
a-L-RhapIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RhaSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE DEPOSITED IN THE SEQUENCE DATABASE.

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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: 2.4 Å3/Da / Density % sol: 48.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: 15% PEG8000, 50mM potassium phosphate, 20mM rhamnose, pH4.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Oct 7, 2003 / Details: mirrors
RadiationMonochromator: confocal mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. all: 39127 / Num. obs: 37718 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.053 / Net I/σ(I): 30.5
Reflection shellResolution: 1.8→1.86 Å / Mean I/σ(I) obs: 8.1 / Num. unique all: 3439 / Rsym value: 0.245 / % possible all: 89.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZX0

2zx0


Resolution: 1.8→29.95 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.896 / SU B: 3.812 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.153 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25623 1885 5 %RANDOM
Rwork0.20579 ---
obs0.20825 35818 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.366 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2---0.59 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3024 0 53 493 3570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213141
X-RAY DIFFRACTIONr_angle_refined_deg1.3641.9724265
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.5675408
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.3724.225142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg7.44815559
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.2451526
X-RAY DIFFRACTIONr_chiral_restr0.0860.2480
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022332
X-RAY DIFFRACTIONr_nbd_refined0.170.21234
X-RAY DIFFRACTIONr_nbtor_refined0.2970.22121
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0970.2357
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1260.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.237
X-RAY DIFFRACTIONr_mcbond_it0.5811.52055
X-RAY DIFFRACTIONr_mcangle_it0.59623174
X-RAY DIFFRACTIONr_scbond_it1.05331237
X-RAY DIFFRACTIONr_scangle_it1.5454.51081
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 116 -
Rwork0.247 2365 -
obs--100 %

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