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- PDB-1byf: STRUCTURE OF TC14; A C-TYPE LECTIN FROM THE TUNICATE POLYANDROCAR... -

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Basic information

Entry
Database: PDB / ID: 1byf
TitleSTRUCTURE OF TC14; A C-TYPE LECTIN FROM THE TUNICATE POLYANDROCARPA MISAKIENSIS
ComponentsPROTEIN (POLYANDROCARPA LECTIN)
KeywordsSUGAR BINDING PROTEIN / C-TYPE LECTIN / GALACTOSE-SPECIFIC
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
ACETATE ION / Lectin
Similarity search - Component
Biological speciesPolyandrocarpa misakiensis (invertebrata)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 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 14, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 23, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_asym_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.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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: 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: PROTEIN (POLYANDROCARPA LECTIN)
B: PROTEIN (POLYANDROCARPA LECTIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,12419
Polymers28,0852
Non-polymers1,03917
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-212 kcal/mol
Surface area10640 Å2
MethodPISA, PQS
2
A: PROTEIN (POLYANDROCARPA LECTIN)
hetero molecules

B: PROTEIN (POLYANDROCARPA LECTIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,12419
Polymers28,0852
Non-polymers1,03917
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
Buried area2440 Å2
ΔGint-233 kcal/mol
Surface area12100 Å2
MethodPISA
3
B: PROTEIN (POLYANDROCARPA LECTIN)
hetero molecules

A: PROTEIN (POLYANDROCARPA LECTIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,12419
Polymers28,0852
Non-polymers1,03917
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
Buried area2760 Å2
ΔGint-226 kcal/mol
Surface area11780 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: (0.1615, -0.0535, -0.9854), (-0.0478, -0.9978, 0.0463), (-0.9857, 0.0396, -0.1637)
Vector: 45.192, 49.1087, 50.4948)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 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

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Non-polymers , 5 types, 296 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 48 %
Crystal growpH: 6.5
Details: PROTEIN WAS CRYSTALLIZED FROM 7% PEG 8000, 0.2 M ZN(ACETATE) AND 100 MM NA( CACODYLATE), 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: Apr 15, 1998 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→52.7 Å / Num. obs: 20632 / % possible obs: 95.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 17.63 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 8.3
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 4 / Rsym value: 0.185 / % possible all: 87.9
Reflection
*PLUS
Num. measured all: 115502
Reflection shell
*PLUS
% possible obs: 87.9 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2→35 Å / SU B: 3.8 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.17
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
Rfree0.25 1039 5.3 %RANDOM
Rwork0.207 ---
obs-19550 96 %-
Displacement parametersBiso mean: 20 Å2
Refinement stepCycle: LAST / Resolution: 2→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1928 0 39 279 2246
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0060.02
X-RAY DIFFRACTIONp_angle_d0.0230.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.020.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.8262
X-RAY DIFFRACTIONp_mcangle_it1.4533
X-RAY DIFFRACTIONp_scbond_it0.9782
X-RAY DIFFRACTIONp_scangle_it1.5473
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.0990.15
X-RAY DIFFRACTIONp_singtor_nbd0.1680.3
X-RAY DIFFRACTIONp_multtor_nbd0.1970.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1340.3
X-RAY DIFFRACTIONp_planar_tor3.17
X-RAY DIFFRACTIONp_staggered_tor14.615
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor34.920
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / σ(F): 0 / Rfactor obs: 0.206 / Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 20 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.04
X-RAY DIFFRACTIONp_planar_d0.05
X-RAY DIFFRACTIONp_chiral_restr0.15
X-RAY DIFFRACTIONp_mcbond_it2
X-RAY DIFFRACTIONp_scbond_it2
X-RAY DIFFRACTIONp_mcangle_it3
X-RAY DIFFRACTIONp_scangle_it3

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