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- PDB-1c1f: LIGAND-FREE CONGERIN I -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1c1f
TitleLIGAND-FREE CONGERIN I
ComponentsPROTEIN (CONGERIN I)
KeywordsSUGAR BINDING PROTEIN / GALECTIN / LECTIN / BETA-GALACTOSE-BINDING
Function / homology
Function and homology information


laminin binding / carbohydrate binding / collagen-containing extracellular matrix / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsShirai, T. / Mitsuyama, C. / Niwa, Y. / Matsui, Y. / Hotta, H. / Yamane, T. / Kamiya, H. / Ishii, C. / Ogawa, T. / Muramoto, K.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: High-resolution structure of the conger eel galectin, congerin I, in lactose-liganded and ligand-free forms: emergence of a new structure class by accelerated evolution.
Authors: Shirai, T. / Mitsuyama, C. / Niwa, Y. / Matsui, Y. / Hotta, H. / Yamane, T. / Kamiya, H. / Ishii, C. / Ogawa, T. / Muramoto, K.
History
DepositionMar 3, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 8, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 20, 2016Group: Database references
Revision 1.4Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (CONGERIN I)


Theoretical massNumber of molelcules
Total (without water)15,3561
Polymers15,3561
Non-polymers00
Water1,45981
1
A: PROTEIN (CONGERIN I)

A: PROTEIN (CONGERIN I)


Theoretical massNumber of molelcules
Total (without water)30,7122
Polymers30,7122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area2470 Å2
ΔGint-15 kcal/mol
Surface area11710 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)94.340, 36.920, 40.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PROTEIN (CONGERIN I)


Mass: 15356.081 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE-RECOGNITION-DOMAIN / Source method: isolated from a natural source / Source: (natural) Conger myriaster (whitespotted conger) / Secretion: NON-CLASSICAL / Tissue: SKIN MUCUS / References: UniProt: P26788
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.3 Å3/Da / Density % sol: 46.57 %
Crystal growpH: 9 / Details: pH 9.0
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 %(w/v)PEG60001reservoir
20.1 MTris-HCl1reservoir
320 mg/mlprotein1drop
410 mMTris-HCl1drop

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 17489 / % possible obs: 91.1 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.046
Reflection shellResolution: 1.6→1.66 Å / % possible all: 76.1
Reflection shell
*PLUS
% possible obs: 76.1 %

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→8 Å / Cross valid method: THROUGHOUT / σ(F): 3
Details: SIDE-CHAINS OF SER123 AND LEU124 ARE MODELED AS ALTERNATIVE CONFORMERS.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 855 5 %RANDOM
Rwork0.201 ---
obs-17099 85 %-
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1078 0 0 81 1159
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor fileSerial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
σ(F): 3 / % reflection Rfree: 5 % / Rfactor obs: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg2.6
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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