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- PDB-1jzn: crystal structure of a galactose-specific C-type lectin -

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Basic information

Entry
Database: PDB / ID: 1jzn
Titlecrystal structure of a galactose-specific C-type lectin
ComponentsGalactose-specific lectin
KeywordsSUGAR BINDING PROTEIN / C-type lectin / protein-disaccharide complex
Function / homology
Function and homology information


carbohydrate binding / extracellular region / metal ion binding
Similarity search - Function
C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold ...C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
beta-lactose / C-type lectin Cal
Similarity search - Component
Biological speciesCrotalus atrox (western diamondback rattlesnake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWalker, J.R. / Nagar, B. / Young, N.M. / Hirama, T. / Rini, J.M.
Citation
Journal: Biochemistry / Year: 2004
Title: X-ray Crystal Structure of a Galactose-Specific C-Type Lectin Possessing a Novel Decameric Quaternary Structure.
Authors: Walker, J.R. / Nagar, B. / Young, N.M. / Hirama, T. / Rini, J.M.
#1: Journal: Biochem.J. / Year: 1984
Title: Isolation and characterization of three Ca2+-dependent beta-galactoside-specific lectins from snake venoms
Authors: Gartner, T.K. / Ogilvie, M.L.
#2: Journal: J.Biol.Chem. / Year: 1991
Title: Complete primary structure of a galactose-specific lectin from the venom of the rattlesnake Crotalus atrox. Homologies with Ca2(+)-dependent-type lectins
Authors: Hirabayashi, J.T. / Kusunoki, T. / Kasai, K.
History
DepositionSep 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galactose-specific lectin
B: Galactose-specific lectin
C: Galactose-specific lectin
D: Galactose-specific lectin
E: Galactose-specific lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,62421
Polymers81,5625
Non-polymers2,06216
Water9,710539
1
A: Galactose-specific lectin
B: Galactose-specific lectin
C: Galactose-specific lectin
D: Galactose-specific lectin
E: Galactose-specific lectin
hetero molecules

A: Galactose-specific lectin
B: Galactose-specific lectin
C: Galactose-specific lectin
D: Galactose-specific lectin
E: Galactose-specific lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,24842
Polymers163,12410
Non-polymers4,12532
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area23590 Å2
ΔGint-257 kcal/mol
Surface area58830 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)63.309, 178.486, 137.832
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a decamer generated from the pentamer in the asymetric unit by the operation -x, y, -z + 1/2.

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Components

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Protein / Sugars , 2 types, 10 molecules ABCDE

#1: Protein
Galactose-specific lectin / RSL (Rattlesnake lectin)


Mass: 16312.377 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Details: Isolated from venom
Source: (natural) Crotalus atrox (western diamondback rattlesnake)
References: UniProt: P21963
#2: Polysaccharide
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 550 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 539 / 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: 2.39 Å3/Da / Density % sol: 48.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Na acetate pH 4.6, 50 mM lactose, 40 mM CaCl2, 1.5 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15-7.5 mg/mlprotein1drop
210 mMTris1droppH8.0
31 mM1dropCaCl2
4100 mMlactose1drop
51.3-1.5 M1reservoirNaCl
61.3-1.5 Msodium acetate1reservoirpH4.6
740 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.8931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 9, 1999
RadiationMonochromator: Horizontally Focused, 3.8 degree asymmetrically cut Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8931 Å / Relative weight: 1
ReflectionResolution: 2.2→37.46 Å / Num. all: 38575 / Num. obs: 38575 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.1 Å2 / Rsym value: 0.063
Reflection shellResolution: 2.2→2.25 Å / Rsym value: 0.15 / % possible all: 80.5
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 40 Å / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 79.8 % / Rmerge(I) obs: 0.156

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
CNS0.9refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→37.46 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 4172349.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Positions of sulfur atoms of residue C86 in all five protein molecules were fixed during refinement as these atoms make disulfide bonds with crystallographically related molecules.
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1170 3 %RANDOM
Rwork0.198 ---
all0.198 38575 --
obs0.198 38575 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.574 Å2 / ksol: 0.358084 e/Å3
Displacement parametersBiso mean: 34.9 Å2
Baniso -1Baniso -2Baniso -3
1-3.08 Å20 Å20 Å2
2--5.15 Å20 Å2
3----8.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.2→37.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5730 0 126 539 6395
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it1.71.5
X-RAY DIFFRACTIONc_mcangle_it2.562
X-RAY DIFFRACTIONc_scbond_it2.782
X-RAY DIFFRACTIONc_scangle_it3.892.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.279 166 3 %
Rwork0.211 5446 -
obs-5446 85.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4CIS_PEPTIDE_PTX8.PARAM
X-RAY DIFFRACTION5CARBOHYDRATE.PARAM
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 40 Å / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85

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