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- PDB-3dui: Crystal structure of the oxidized CG-1B: an adhesion/growth-regul... -

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Basic information

Entry
Database: PDB / ID: 3dui
TitleCrystal structure of the oxidized CG-1B: an adhesion/growth-regulatory lectin from chicken
ComponentsBeta-galactoside-binding lectin
KeywordsSUGAR BINDING PROTEIN / CARBOHYDRATE-BINDING PROTEINS / GALACTOSIDES / GALECTIN / Acetylation / Lectin
Function / homology
Function and homology information


Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / laminin binding / carbohydrate binding / extracellular space
Similarity search - Function
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
BETA-MERCAPTOETHANOL / Beta-galactoside-binding lectin
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRomero, A. / Lopez-Lucendo, M.I.F. / Solis, D. / Gabius, H.-J.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Homodimeric chicken galectin CG-1B (C-14): Crystal structure and detection of unique redox-dependent shape changes involving inter- and intrasubunit disulfide bridges by gel filtration, ...Title: Homodimeric chicken galectin CG-1B (C-14): Crystal structure and detection of unique redox-dependent shape changes involving inter- and intrasubunit disulfide bridges by gel filtration, ultracentrifugation, site-directed mutagenesis, and peptide mass fingerprinting
Authors: Lopez-Lucendo, M.F. / Solis, D. / Saiz, J.L. / Kaltner, H. / Russwurm, R. / Andre, S. / Gabius, H.-J. / Romero, A.
History
DepositionJul 17, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-galactoside-binding lectin
B: Beta-galactoside-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3184
Polymers30,1622
Non-polymers1562
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-7 kcal/mol
Surface area12320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.590, 107.640, 35.830
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 Beta-galactoside-binding lectin / 14 kDa lectin / C-14 / CG-1B (CG-14)


Mass: 15081.107 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / References: UniProt: P07583
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.29 Å3/Da / Density % sol: 46.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 30% (v/v) PEG 8000, 1% beta-mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 5, 2007
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.1→25.35 Å / Num. all: 16859 / Num. obs: 16792 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 31.1 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.048 / Net I/σ(I): 6.9
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2384 / Rsym value: 0.28 / % possible all: 99.3

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Processing

Software
NameVersionClassification
DNAdata collection
AMoREphasing
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QMJ

1qmj


Resolution: 2.1→25.35 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.286 818 -RANDOM
Rwork0.238 ---
obs0.238 16792 99.4 %-
all-16752 --
Displacement parametersBiso mean: 39 Å2
Baniso -1Baniso -2Baniso -3
1--7.76 Å20 Å20 Å2
2---19.09 Å20 Å2
3---26.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.1→25.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2084 0 8 98 2190
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_mcbond_it1.4
X-RAY DIFFRACTIONc_mcangle_it2.3
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.033
RfactorNum. reflection% reflection
Rfree0.366 121 -
Rwork0.368 --
obs-2610 99.3 %

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