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- PDB-2dyc: Crystal structure of the N-terminal domain of mouse galectin-4 -

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Basic information

Entry
Database: PDB / ID: 2dyc
TitleCrystal structure of the N-terminal domain of mouse galectin-4
ComponentsGalectin-4
KeywordsSUGAR BINDING PROTEIN / GAL-BIND LECTIN / GALECTIN / SUGAR BINDING / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


antibacterial peptide biosynthetic process / galactoside binding / : / carbohydrate binding / defense response to bacterium / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsKato-Murayama, M. / Murayama, K. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of the N-terminal domain of mouse galectin-4
Authors: Kato-Murayama, M. / Murayama, K. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionSep 8, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Galectin-4


Theoretical massNumber of molelcules
Total (without water)18,1491
Polymers18,1491
Non-polymers00
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Galectin-4
x 8


Theoretical massNumber of molelcules
Total (without water)145,1948
Polymers145,1948
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_655-x+1,y,-z1
crystal symmetry operation6_565x,-y+1,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area16820 Å2
ΔGint-85 kcal/mol
Surface area46180 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)92.053, 92.053, 132.908
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Galectin-4 / Lactose-binding lectin 4


Mass: 18149.283 Da / Num. of mol.: 1 / Fragment: residues 9-159
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: cell-free protein synthesis / Plasmid: PX051128-10 / References: UniProt: Q8K419
#2: Water ChemComp-HOH / water


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

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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: 3.88 Å3/Da / Density % sol: 68.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.4M Ammonium Sulfate, 12% Glycerol, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9790, 0.9794, 0.970
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 7, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97941
30.971
ReflectionResolution: 2.4→50 Å / Num. obs: 11598 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 9 % / Biso Wilson estimate: 21.5 Å2 / Rsym value: 0.109 / Net I/σ(I): 17.2
Reflection shellResolution: 2.4→2.49 Å / Rsym value: 0.363 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→46.5 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2219713.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1190 10.3 %RANDOM
Rwork0.22 ---
obs0.22 11514 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.2163 Å2 / ksol: 0.37361 e/Å3
Displacement parametersBiso mean: 27.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.4→46.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1182 0 0 81 1263
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.581.5
X-RAY DIFFRACTIONc_mcangle_it2.672
X-RAY DIFFRACTIONc_scbond_it2.432
X-RAY DIFFRACTIONc_scangle_it3.612.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.292 176 9.4 %
Rwork0.234 1697 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top

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