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- PDB-1is5: Ligand free Congerin II -

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Basic information

Entry
Database: PDB / ID: 1is5
TitleLigand free Congerin II
ComponentsCongerin II
KeywordsSUGAR BINDING PROTEIN / 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: 2 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 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Congerin II


Theoretical massNumber of molelcules
Total (without water)15,3541
Polymers15,3541
Non-polymers00
Water1,31573
1
A: Congerin II

A: Congerin II


Theoretical massNumber of molelcules
Total (without water)30,7082
Polymers30,7082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)61.200, 61.200, 80.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.47 Å3/Da / Density % sol: 50.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: magnesium sulfate, sodium citrate, 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
30.1 MTris-HCl1droppH6.5
41.6 M1reservoirMgSO4
50.1 MTris-HCl1reservoirpH6.5

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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: Jan 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→99 Å / Num. all: 10908 / Num. obs: 10908 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.04 / Net I/σ(I): 40.6
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.086 / Mean I/σ(I) obs: 23.5 / Num. unique all: 1058 / % possible all: 98.5
Reflection
*PLUS
Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 98.5 % / Num. unique obs: 1058 / Rmerge(I) obs: 0.086

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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: 2→8 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 506 4.8 %RANDOM
Rwork0.168 ---
all0.171 10636 --
obs0.17 10529 --
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1078 0 0 73 1151
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_angle_deg2.9
X-RAY DIFFRACTIONx_dihedral_angle_d26.7
X-RAY DIFFRACTIONx_improper_angle_d1
LS refinement shellResolution: 2→2.07 Å
RfactorNum. reflection% reflection
Rfree0.29 51 5.2 %
Rwork0.182 --
obs-973 -
Refinement
*PLUS
Rfactor all: 0.171 / Rfactor obs: 0.17 / Rfactor Rfree: 0.228 / Rfactor Rwork: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1
LS refinement shell
*PLUS
Rfactor Rfree: 0.29 / Rfactor Rwork: 0.182

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