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- PDB-1tlg: STRUCTURE OF A TUNICATE C-TYPE LECTIN COMPLEXED WITH D-GALACTOSE -

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Basic information

Entry
Database: PDB / ID: 1tlg
TitleSTRUCTURE OF A TUNICATE C-TYPE LECTIN COMPLEXED WITH D-GALACTOSE
ComponentsPOLYANDROCARPA LECTIN
KeywordsLECTIN / C-TYPE LECTIN / GALACTOSE-SPECIFIC / CARBOHYDRATE BINDING
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
TC14-like, C-type lectin-like domain / : / 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) ...TC14-like, C-type lectin-like domain / : / 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-D-galactopyranose / Lectin
Similarity search - Component
Biological speciesPolyandrocarpa misakiensis (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPoget, S.F. / Legge, G.B. / Bycroft, M. / Williams, R.L.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: The structure of a tunicate C-type lectin from Polyandrocarpa misakiensis complexed with D -galactose.
Authors: Poget, S.F. / Legge, G.B. / Proctor, M.R. / Butler, P.J. / Bycroft, M. / Williams, R.L.
#1: Journal: Roux'S Arch.Dev.Biol. / Year: 1995
Title: Expression of Genes for 2 C-Type Lectins During Budding of the Ascidian Polyandrocarpa-Misakiensis
Authors: Shimada, M. / Fujiwara, S. / Kawamura, K.
#2: Journal: DEVELOPMENT / Year: 1991
Title: Budding-Specific Lectin Induced in Epithelial Cells is an Extracellular Matrix Component for Stem Cell Aggregation in Tunicates
Authors: Kawamura, K. / Fujiwara, S. / Sugino, Y.M.
#3: Journal: J.Biol.Chem. / Year: 1990
Title: A Calcium-Dependent Galactose-Binding Lectin from the Tunicate Polyandrocarpa Misakiensis. Isolation, Characterization, and Amino Acid Sequence
Authors: Suzuki, T. / Takagi, T. / Furukohri, T. / Kawamura, K. / Nakauchi, M.
History
DepositionOct 16, 1998Processing site: BNL
Revision 1.0Jul 23, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 9, 2023Group: Database references / Refinement description / Structure summary
Category: chem_comp / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POLYANDROCARPA LECTIN
B: POLYANDROCARPA LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,93313
Polymers28,0852
Non-polymers84811
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-130 kcal/mol
Surface area10800 Å2
MethodPISA
2
A: POLYANDROCARPA LECTIN
hetero molecules

B: POLYANDROCARPA LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,93313
Polymers28,0852
Non-polymers84811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
Buried area1530 Å2
ΔGint-151 kcal/mol
Surface area12280 Å2
MethodPISA
3
B: POLYANDROCARPA LECTIN
hetero molecules

A: POLYANDROCARPA LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,93313
Polymers28,0852
Non-polymers84811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
Buried area1630 Å2
ΔGint-146 kcal/mol
Surface area12180 Å2
MethodPISA
4
A: POLYANDROCARPA LECTIN
hetero molecules

B: POLYANDROCARPA LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,93313
Polymers28,0852
Non-polymers84811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
Buried area1580 Å2
ΔGint-137 kcal/mol
Surface area12140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.180, 66.450, 85.900
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: (0.1639, -0.0514, -0.9851), (-0.0513, -0.9977, 0.0435), (-0.9851, 0.0435, -0.1662)
Vector: 45.0379, 49.2402, 50.4428)

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Components

#1: Protein POLYANDROCARPA LECTIN / TC14


Mass: 14042.505 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Polyandrocarpa misakiensis (invertebrata)
Description: SYNTHETIC GENE / Plasmid: PRSETA-LEC
Cellular location (production host): CYTOPLASM AS INCLUSION BODIES
Gene (production host): TC14-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): C41 / References: UniProt: P16108
#2: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.8 Å3/Da / Density % sol: 48 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 17 ℃ / pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.4 mMprotein1drop
212.5 mM1dropCaCl2
32.5 mMD-galactose1drop
410 mMTris1drop
525 mM1dropNaCl
67 %(w/v)PEG80001reservoir
70.2 M1reservoirZn(ac)2v2H2O
80.1 Msodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1998 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→16.4 Å / Num. obs: 16111 / % possible obs: 99.1 % / Redundancy: 6.7 % / Biso Wilson estimate: 23.14 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 11.6
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.171 / Mean I/σ(I) obs: 4.4 / Rsym value: 0.171 / % possible all: 83.8
Reflection
*PLUS
Num. measured all: 108587
Reflection shell
*PLUS
% possible obs: 83.8 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BYF

1byf


Resolution: 2.2→26 Å / SU B: 6.24 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.28 / ESU R Free: 0.23
Details: ELECTRON DENSITY FOR RESIDUE MET A 1 AND MET B 1 IS PRESENT, BUT MODELLING WITH ACCEPTABLE GEOMETRY WAS NOT POSSIBLE. A CHAIN OF 5 VERY HIGH ELECTRON DENSITY SPHERES ADJACENT AND ORTHOGONAL ...Details: ELECTRON DENSITY FOR RESIDUE MET A 1 AND MET B 1 IS PRESENT, BUT MODELLING WITH ACCEPTABLE GEOMETRY WAS NOT POSSIBLE. A CHAIN OF 5 VERY HIGH ELECTRON DENSITY SPHERES ADJACENT AND ORTHOGONAL TO THE SIDE-CHAIN OF ASP A 2 AND ASP B 2 WAS MODELLED AS ZN-HOH-ZN-HOH-ZN, BUT THE RESOLUTION IS NOT HIGH ENOUGH FOR UNAMBIGUOUS CHARACTERISATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.269 808 5.3 %RANDOM
Rwork0.211 ---
obs-15259 99.1 %-
Displacement parametersBiso mean: 25.5 Å2
Refinement stepCycle: LAST / Resolution: 2.2→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1928 0 33 243 2204
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0070.02
X-RAY DIFFRACTIONp_angle_d0.0250.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0220.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.062
X-RAY DIFFRACTIONp_mcangle_it1.8493
X-RAY DIFFRACTIONp_scbond_it1.1342
X-RAY DIFFRACTIONp_scangle_it1.8053
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.0990.15
X-RAY DIFFRACTIONp_singtor_nbd0.170.3
X-RAY DIFFRACTIONp_multtor_nbd0.2050.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1390.3
X-RAY DIFFRACTIONp_planar_tor3.47
X-RAY DIFFRACTIONp_staggered_tor13.915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor34.720
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS

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