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- PDB-1bkz: CRYSTAL STRUCTURE OF HUMAN GALECTIN-7 -

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Basic information

Entry
Database: PDB / ID: 1bkz
TitleCRYSTAL STRUCTURE OF HUMAN GALECTIN-7
ComponentsGALECTIN-7
KeywordsLECTIN / GALAPTIN / GALECTIN / CARBOHYDRATE BINDING
Function / homology
Function and homology information


Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / heterophilic cell-cell adhesion / carbohydrate binding / apoptotic process / extracellular space / extracellular exosome / nucleus / cytoplasm
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsLeonidas, D.D. / Acharya, K.R.
CitationJournal: Biochemistry / Year: 1998
Title: Structural basis for the recognition of carbohydrates by human galectin-7.
Authors: Leonidas, D.D. / Vatzaki, E.H. / Vorum, H. / Celis, J.E. / Madsen, P. / Acharya, K.R.
History
DepositionJul 13, 1998Processing site: BNL
Revision 1.0Nov 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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: GALECTIN-7
B: GALECTIN-7


Theoretical massNumber of molelcules
Total (without water)29,9322
Polymers29,9322
Non-polymers00
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.230, 65.340, 73.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.276136, -0.61257, -0.740613), (-0.717676, -0.381131, 0.582821), (-0.639289, 0.692458, -0.334382)
Vector: 99.577, 47.91, 57.968)

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Components

#1: Protein GALECTIN-7


Mass: 14965.850 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Plasmid: BL21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P47929
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 43 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.1
Details: CRYSTALS WERE GROWN USING THE HANGING DROP METHOD FROM DROPS CONTAINING 9 MG/ML PROTEIN AT PH 8.1 IN 50 MM SODIUM PHOSPHATE BUFFER, 0.3 M SODIUM CHLORIDE, 20 MM IMIDAZOLE, AND 8.5% PEG 3350. ...Details: CRYSTALS WERE GROWN USING THE HANGING DROP METHOD FROM DROPS CONTAINING 9 MG/ML PROTEIN AT PH 8.1 IN 50 MM SODIUM PHOSPHATE BUFFER, 0.3 M SODIUM CHLORIDE, 20 MM IMIDAZOLE, AND 8.5% PEG 3350. DROPS WERE EQUILIBRATED AGAINST RESERVOIRS CONTAINING 50 MM SODIUM PHOSPHATE BUFFER, 0.3 M SODIUM CHLORIDE, 20 MM IMIDAZOLE, AND 17% PEG 3350., vapor diffusion - hanging drop
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
19 mg/mlprotein1drop
250 mMsodium phosphate1drop
30.3 M1dropNaCl
420 mMimidazol1drop
58.5 %PEG33501drop
650 mMsodium phosphate1reservoir
70.3 M1reservoirNaCl
820 mMimidazole1reservoir
917 %PEG33501reservoir

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1997 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 20244 / % possible obs: 95.4 % / Observed criterion σ(I): -3 / Redundancy: 10.6 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 10
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 4.5 / Rsym value: 0.449 / % possible all: 81.5

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Processing

Software
NameVersionClassification
SHARPphasing
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.26 981 4.8 %RANDOM
Rwork0.194 ---
obs0.194 20239 95.5 %-
Displacement parametersBiso mean: 35.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2116 0 0 89 2205
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d30.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.79
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.951.5
X-RAY DIFFRACTIONx_mcangle_it3.212
X-RAY DIFFRACTIONx_scbond_it3.412
X-RAY DIFFRACTIONx_scangle_it5.442.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.292 151 5.1 %
Rwork0.289 2788 -
obs--84.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REPTOPHCSDX.PR
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg30.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.79

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