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- PDB-6tig: Structure of the N terminal domain of Bc2L-C lectin (1-131) in co... -

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Basic information

Entry
Database: PDB / ID: 6tig
TitleStructure of the N terminal domain of Bc2L-C lectin (1-131) in complex with Globo H (H-type 3) antigen
ComponentsLectin
KeywordsSUGAR BINDING PROTEIN / Lectin / TNF-like / Globo H
Function / homologyLectin Bc2l-C, N-terminal / : / Bc2l-C, N-terminal domain / Calcium-mediated lectin / Calcium-mediated lectin superfamily / Fucose-binding lectin II (PA-IIL) / identical protein binding / Lectin
Function and homology information
Biological speciesBurkholderia cenocepacia J2315 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsVarrot, A. / Bermeo, R.
Funding support France, 2items
OrganizationGrant numberCountry
European Union765581 France
French National Research AgencyANR-15-IDEX-02 France
CitationJournal: Molecules / Year: 2020
Title: BC2L-C N-Terminal Lectin Domain Complexed with Histo Blood Group Oligosaccharides Provides New Structural Information.
Authors: Bermeo, R. / Bernardi, A. / Varrot, A.
History
DepositionNov 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
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 / 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_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn
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 / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_type / chem_comp ...atom_type / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Lectin
BBB: Lectin
CCC: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4326
Polymers42,0333
Non-polymers2,3993
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10590 Å2
ΔGint17 kcal/mol
Surface area14120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.368, 42.882, 102.648
Angle α, β, γ (deg.)90.000, 96.007, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains AAA BBB
21Chains AAA CCC
31Chains BBB CCC

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Components

#1: Protein Lectin


Mass: 14010.936 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: N terminal domain
Source: (gene. exp.) Burkholderia cenocepacia J2315 (bacteria)
Gene: BCAM0185 / Production host: Escherichia coli (E. coli) / References: UniProt: B4EH86
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose- ...alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-alpha-D-galactopyranose


Type: oligosaccharide / Mass: 691.630 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2DGalpb1-3DGalpNAcb1-3DGalpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,4,3/[a2112h-1a_1-5][a2112h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][a1221m-1a_1-5]/1-2-3-4/a3-b1_b3-c1_c2-d1WURCSPDB2Glycan 1.1.0
[][a-D-Galp]{[(3+1)][b-D-GalpNAc]{[(3+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose- ...alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 853.771 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2DGalpb1-3DGalpNAcb1-3DGalpa1-4DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2112h-1b_1-5][a2112h-1a_1-5][a2112h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-3-1-4/a4-b1_b3-c1_c3-d1_d2-e1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(4+1)][a-D-Galp]{[(3+1)][b-D-GalpNAc]{[(3+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.95 Å3/Da / Density % sol: 37.01 % / Description: Plate
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: Sodium citrate 1.2M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.9→37.1 Å / Num. obs: 25081 / % possible obs: 97.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 17.8 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.071 / Rrim(I) all: 0.105 / Net I/σ(I): 8.7
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1628 / CC1/2: 0.861 / Rpim(I) all: 0.32 / Rrim(I) all: 0.486 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimless0.7.3data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TID

6tid


Resolution: 1.9→37.1 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.265 / SU ML: 0.125 / Cross valid method: FREE R-VALUE / ESU R: 0.195 / ESU R Free: 0.171
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2265 1552 6.188 %
Rwork0.1652 --
all0.169 --
obs-25080 97.546 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.643 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å2-0 Å20.157 Å2
2---1.499 Å20 Å2
3---2.618 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2951 0 163 287 3401
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0133280
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172994
X-RAY DIFFRACTIONr_angle_refined_deg1.9981.7134528
X-RAY DIFFRACTIONr_angle_other_deg1.4911.6286979
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9865419
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57722.477109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.96515446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.144159
X-RAY DIFFRACTIONr_chiral_restr0.1020.2502
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023575
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02643
X-RAY DIFFRACTIONr_nbd_refined0.2010.2475
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.22830
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21627
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0950.21448
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2205
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0330.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1830.221
X-RAY DIFFRACTIONr_nbd_other0.1890.2100
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2480.223
X-RAY DIFFRACTIONr_mcbond_it2.9442.4841648
X-RAY DIFFRACTIONr_mcbond_other2.9442.4821647
X-RAY DIFFRACTIONr_mcangle_it3.8633.7032071
X-RAY DIFFRACTIONr_mcangle_other3.8633.7062072
X-RAY DIFFRACTIONr_scbond_it3.4092.7731631
X-RAY DIFFRACTIONr_scbond_other3.4052.7731631
X-RAY DIFFRACTIONr_scangle_it4.774.072455
X-RAY DIFFRACTIONr_scangle_other4.774.0712456
X-RAY DIFFRACTIONr_lrange_it6.57530.7793420
X-RAY DIFFRACTIONr_lrange_other6.48330.6393392
X-RAY DIFFRACTIONr_ncsr_local_group_10.070.053935
X-RAY DIFFRACTIONr_ncsr_local_group_20.0730.053939
X-RAY DIFFRACTIONr_ncsr_local_group_30.070.054066
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.2831100.2161758X-RAY DIFFRACTION96.5375
1.949-2.0030.26930.1891637X-RAY DIFFRACTION96.8103
2.003-2.0610.267840.1771691X-RAY DIFFRACTION96.8358
2.061-2.1240.2481070.1721554X-RAY DIFFRACTION96.9078
2.124-2.1940.234990.1671512X-RAY DIFFRACTION96.9314
2.194-2.2710.219950.1461521X-RAY DIFFRACTION97.6435
2.271-2.3560.2391020.1581408X-RAY DIFFRACTION97.4194
2.356-2.4530.254930.181380X-RAY DIFFRACTION97.7439
2.453-2.5620.2551020.1741348X-RAY DIFFRACTION97.973
2.562-2.6870.253930.1681290X-RAY DIFFRACTION98.0851
2.687-2.8320.242700.1551207X-RAY DIFFRACTION98.0799
2.832-3.0030.214740.161142X-RAY DIFFRACTION98.1437
3.003-3.2110.216760.1531074X-RAY DIFFRACTION97.6231
3.211-3.4680.25710.1621008X-RAY DIFFRACTION97.9129
3.468-3.7980.216760.157939X-RAY DIFFRACTION98.7354
3.798-4.2460.175520.134873X-RAY DIFFRACTION98.8248
4.246-4.9010.182580.142743X-RAY DIFFRACTION98.0416
4.901-5.9990.199450.153648X-RAY DIFFRACTION98.5775
5.999-8.4690.175350.204504X-RAY DIFFRACTION98
8.469-37.10.486170.291291X-RAY DIFFRACTION95.356

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