[English] 日本語
Yorodumi
- PDB-6tid: Structure of the N terminal domain of Bc2L-C lectin (1-131) in co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tid
TitleStructure of the N terminal domain of Bc2L-C lectin (1-131) in complex with H-type 1 antigen
ComponentsLectin
KeywordsSUGAR BINDING PROTEIN / Lectin / TNF-like / fucosylated antigen
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 / H type 1 antigen, beta anomer / Lectin
Function and homology information
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.614 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 / 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_special_symmetry / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _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.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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5402
Polymers14,0111
Non-polymers5291
Water2,378132
1
AAA: Lectin
hetero molecules

AAA: Lectin
hetero molecules

AAA: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6216
Polymers42,0333
Non-polymers1,5883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area9340 Å2
ΔGint3 kcal/mol
Surface area13700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.696, 42.696, 308.584
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11AAA-301-

HOH

21AAA-313-

HOH

31AAA-395-

HOH

41AAA-416-

HOH

51AAA-418-

HOH

61AAA-425-

HOH

-
Components

#1: Protein Lectin


Mass: 14010.936 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610) (bacteria)
Strain: ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610
Gene: BCAM0185 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: B4EH86
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose / H type 1 antigen / beta anomer


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 529.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: H type 1 antigen, beta anomer
DescriptorTypeProgram
LFucpa1-2DGalpb1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][a1221m-1a_1-5]/1-2-3/a3-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.45 % / Description: Thick square
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.2 M Na citrate pH 7.0 cryoprotected in 2.5 M sodium malonate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.98096 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98096 Å / Relative weight: 1
ReflectionResolution: 1.61→36.71 Å / Num. obs: 14606 / % possible obs: 99.7 % / Redundancy: 7.8 % / Biso Wilson estimate: 18.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.027 / Rrim(I) all: 0.056 / Net I/σ(I): 23.9
Reflection shellResolution: 1.61→1.64 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 712 / CC1/2: 0.874 / Rpim(I) all: 0.32 / Rrim(I) all: 0.643 / % possible all: 97.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
Aimless0.7.3data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2wq4

2wq4


Resolution: 1.614→36.71 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.606 / SU ML: 0.057 / Cross valid method: FREE R-VALUE / ESU R: 0.093 / ESU R Free: 0.097
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2027 751 5.142 %
Rwork0.1583 --
all0.161 --
obs-14605 99.652 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.654 Å2
Baniso -1Baniso -2Baniso -3
1--0.186 Å2-0.093 Å20 Å2
2---0.186 Å20 Å2
3---0.603 Å2
Refinement stepCycle: LAST / Resolution: 1.614→36.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms967 0 36 132 1135
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131056
X-RAY DIFFRACTIONr_bond_other_d0.0010.017971
X-RAY DIFFRACTIONr_angle_refined_deg1.7791.6911454
X-RAY DIFFRACTIONr_angle_other_deg1.5551.6122257
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0335134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.22522.536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.05215146
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.944153
X-RAY DIFFRACTIONr_chiral_restr0.0990.2159
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021158
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02208
X-RAY DIFFRACTIONr_nbd_refined0.2080.2148
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.2859
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2517
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0920.2488
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.287
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1510.213
X-RAY DIFFRACTIONr_nbd_other0.1730.284
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1960.237
X-RAY DIFFRACTIONr_mcbond_it1.7891.842537
X-RAY DIFFRACTIONr_mcbond_other1.7821.836536
X-RAY DIFFRACTIONr_mcangle_it2.5262.732672
X-RAY DIFFRACTIONr_mcangle_other2.5262.739673
X-RAY DIFFRACTIONr_scbond_it2.2852.024519
X-RAY DIFFRACTIONr_scbond_other2.2832.024520
X-RAY DIFFRACTIONr_scangle_it3.3892.976782
X-RAY DIFFRACTIONr_scangle_other3.3872.976783
X-RAY DIFFRACTIONr_lrange_it5.04722.7991113
X-RAY DIFFRACTIONr_lrange_other4.89722.2381091
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.614-1.6560.344510.2319990.23710600.90.92999.05660.231
1.656-1.7010.265460.1939830.19610300.9280.94999.90290.193
1.701-1.7510.23680.1769200.1799880.9440.9561000.176
1.751-1.8040.258550.1729290.1779850.9250.95199.89850.172
1.804-1.8630.234490.1679000.1719500.940.95599.89470.167
1.863-1.9290.238440.1668680.1699120.9430.9581000.166
1.929-2.0010.198370.1758580.1768950.9460.9571000.175
2.001-2.0830.225480.1647910.1678420.9490.96599.64370.164
2.083-2.1750.167360.1617940.1618320.9640.96699.75960.161
2.175-2.2810.194310.1457470.1477780.960.9721000.145
2.281-2.4040.171410.1527250.1537680.9710.9799.73960.152
2.404-2.5490.223420.1566730.167160.9490.96499.86030.156
2.549-2.7240.199470.1666230.1686710.9590.96399.8510.166
2.724-2.9410.185370.1515910.1536310.9580.96799.52460.151
2.941-3.2190.194280.1515680.1545970.9560.96499.83250.151
3.219-3.5960.231260.1465060.155380.9550.97198.88480.146
3.596-4.1460.124220.1284570.1284810.9820.97799.58420.128
4.146-5.0610.11200.1073940.1074150.9860.98899.7590.107
5.061-7.090.276150.1723290.1763450.9730.97599.71010.172
7.09-36.7130.29380.2741980.2752170.940.93194.93090.274

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more