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- PDB-2jj6: Crystal structure of the putative carbohydrate recognition domain... -

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Basic information

Entry
Database: PDB / ID: 2jj6
TitleCrystal structure of the putative carbohydrate recognition domain of the human galectin-related protein
ComponentsGALECTIN-RELATED PROTEIN
KeywordsSUGAR BINDING PROTEIN / SUGAR-BINDING PROTEIN / HUMAN / GALECTIN / CARBOHYDRATE RECOGNITION DOMAIN SUGAR-BINDING PROTEIN
Function / homology
Function and homology information


carbohydrate binding
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
Galectin-related protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsThore, S. / Walti, M.A. / Kunzler, M. / Aebi, M.
CitationJournal: Proteins: Struct., Funct., Bioinf. / Year: 2008
Title: Crystal Structure of the Putative Carbohydrate Recognition Domain of Human Galectin-Related Protein
Authors: Walti, M.A. / Thore, S. / Kunzler, M. / Aebi, M.
History
DepositionMar 18, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 20, 2018Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.page_last / _diffrn_source.pdbx_synchrotron_beamline
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GALECTIN-RELATED PROTEIN
B: GALECTIN-RELATED PROTEIN


Theoretical massNumber of molelcules
Total (without water)30,1252
Polymers30,1252
Non-polymers00
Water4,197233
1
A: GALECTIN-RELATED PROTEIN


Theoretical massNumber of molelcules
Total (without water)15,0621
Polymers15,0621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: GALECTIN-RELATED PROTEIN


Theoretical massNumber of molelcules
Total (without water)15,0621
Polymers15,0621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)78.391, 78.391, 89.883
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein GALECTIN-RELATED PROTEIN


Mass: 15062.312 Da / Num. of mol.: 2 / Fragment: CARBOHYDRATE RECOGNITION DOMAIN, RESIDUES 38-171
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q3ZCW2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 48.9 %
Description: ONLY ONE MONOMER FROM THE PDB ENTRY 1BKZ WAS USED IN MOLECULAR REPLACEMENT SEARCHES
Crystal growDetails: TRIS/HCL, PH8.0, 14% PEG6000

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Type: SLS / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 21932 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 24.4
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 4.6 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.2refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BKZ

1bkz


Resolution: 2→25 Å / Rfactor Rfree error: 0.033 / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUN LIKELIHOOD / Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2589 1111 5 %RANDOM
Rwork0.217 ---
obs0.217 21834 99.1 %-
Solvent computationBsol: 66.4 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 51 Å2
Baniso -1Baniso -2Baniso -3
1-10.082 Å20 Å20 Å2
2--10.082 Å20 Å2
3----20.164 Å2
Refine analyzeLuzzati coordinate error obs: 0.278 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.249 Å
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2111 0 0 233 2344
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0106
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_deg2.0437
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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