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- PDB-1is6: MES-Liganded Congerin II -

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Basic information

Entry
Database: PDB / ID: 1is6
TitleMES-Liganded Congerin II
ComponentsCongerin II
KeywordsSUGAR BINDING PROTEIN / MES complex / BETA SANDWICH
Function / homology
Function and homology information


galactoside binding / laminin binding / carbohydrate binding / extracellular space
Similarity search - Function
Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesConger myriaster (whitespotted conger)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsShirai, T. / Matsui, Y. / Shionyu-Mitsuyama, C. / Yamane, T. / Kamiya, H. / Ishii, C. / Ogawa, T. / Muramoto, K.
CitationJournal: J.MOL.BIOL. / Year: 2002
Title: Crystal structure of a conger eel galectin (congerin II) at 1.45 A resolution: Implication for the accelerated evolution of a new ligand-binding site following gene duplication
Authors: Shirai, T. / Matsui, Y. / Shionyu-Mitsuyama, C. / Yamane, T. / Kamiya, H. / Ishii, C. / Ogawa, T. / Muramoto, K.
History
DepositionNov 12, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 27, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Apr 3, 2024Group: Advisory / Derived calculations / Refinement description
Category: pdbx_initial_refinement_model / pdbx_struct_special_symmetry / pdbx_validate_symm_contact

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Congerin II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5492
Polymers15,3541
Non-polymers1951
Water1,24369
1
A: Congerin II
hetero molecules

A: Congerin II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0994
Polymers30,7082
Non-polymers3902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)61.400, 61.400, 80.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-409-

HOH

DetailsThe second part of the biological assembly is generated by the two fold axis : y, x, -z+1.

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Components

#1: Protein Congerin II / BETA-GALACTOSIDE-BINDING LECTIN 2


Mass: 15354.119 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Conger myriaster (whitespotted conger) / Plasmid: pTV118N / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q9YIC2
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.48 Å3/Da / Density % sol: 50.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: magnesium sulfate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.8 M1dropMgSO4
21 %(w/v)protein1drop
30.5 MMES1droppH6.5
41.6 M1reservoirMgSO4
51.0 MMES1reservoirpH6.5

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 25, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→99 Å / Num. all: 17071 / Num. obs: 17071 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.047 / Net I/σ(I): 30.38
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 4.9 / Num. unique all: 1414 / % possible all: 82
Reflection
*PLUS
Rmerge(I) obs: 0.047
Reflection shell
*PLUS
% possible obs: 82 % / Num. unique obs: 1414 / Rmerge(I) obs: 0.194

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Congerin II Lactose and Mes complex

Resolution: 1.7→8 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 748 4.6 %RANDOM
Rwork0.187 ---
all0.192 16778 --
obs0.188 16178 --
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1078 0 12 69 1159
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_angle_deg2.8
X-RAY DIFFRACTIONx_dihedral_angle_d26.6
X-RAY DIFFRACTIONx_improper_angle_d2
LS refinement shellResolution: 1.7→1.76 Å
RfactorNum. reflection% reflection
Rfree0.234 50 4.3 %
Rwork0.237 --
obs-1155 -
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 8 Å / Rfactor all: 0.192 / Rfactor obs: 0.188 / Rfactor Rfree: 0.232 / Rfactor Rwork: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2
LS refinement shell
*PLUS
Rfactor Rfree: 0.234 / Rfactor Rwork: 0.237

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