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- PDB-5g3l: ESCHERICHIA COLI HEAT LABILE ENTEROTOXIN TYPE IIB B-PENTAMER COMP... -

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Basic information

Entry
Database: PDB / ID: 5g3l
TitleESCHERICHIA COLI HEAT LABILE ENTEROTOXIN TYPE IIB B-PENTAMER COMPLEXED WITH SIALYLATED SUGAR
Components(HEAT-LABILE ENTEROTOXIN IIB, B ...) x 2
KeywordsTOXIN / ENTEROTOXIN / ECOLI / B SUBUNIT / SIALIC ACID
Function / homology
Function and homology information


host cell membrane / toxin activity / extracellular region
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #50 / Type II heat-labile enterotoxin, B subunit / Type II heat-labile enterotoxin, B subunit superfamily / Type II heat-labile enterotoxin , B subunit (LT-IIB) / Enterotoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
N-acetyl-alpha-neuraminic acid / Heat-labile enterotoxin IIB, B chain
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsZalem, D. / Benktander, J. / Ribeiro, J.P. / Varrot, A. / Lebens, M. / Imberty, A. / Teneberg, S.
CitationJournal: Biochem.J. / Year: 2016
Title: Biochemical and Structural Characterization of the Novel Sialic Acid-Binding Site of Escherichia Coli Heat-Labile Enterotoxin Lt-Iib.
Authors: Zalem, D. / Ribeiro, J.P. / Varrot, A. / Lebens, M. / Imberty, A. / Teneberg, S.
History
DepositionApr 29, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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 / pdbx_struct_conn_angle / pdbx_validate_close_contact / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.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.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
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. ... SHEET DETERMINATION METHOD: AUTHOR PROVIDED. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: HEAT-LABILE ENTEROTOXIN IIB, B CHAIN
E: HEAT-LABILE ENTEROTOXIN IIB, B CHAIN
F: HEAT-LABILE ENTEROTOXIN IIB, B CHAIN
G: HEAT-LABILE ENTEROTOXIN IIB, B CHAIN
H: HEAT-LABILE ENTEROTOXIN IIB, B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,06414
Polymers53,9395
Non-polymers2,1259
Water10,611589
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15150 Å2
ΔGint-131.4 kcal/mol
Surface area18750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.564, 68.015, 154.513
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.724, 0.649, -0.233), (-0.536, 0.318, -0.782), (-0.434, 0.691, 0.578)-0.48251, 1.35139, -0.08973
2given(0.244, 0.533, -0.81), (-0.214, -0.785, -0.581), (-0.946, 0.315, -0.078)0.47165, 2.1172, 0.34673
3given(0.237, -0.222, -0.946), (0.531, -0.786, 0.317), (-0.814, -0.577, -0.068)1.58405, 1.23582, 0.68622
4given(0.705, -0.556, -0.439), (0.668, 0.314, 0.675), (-0.237, -0.769, 0.593)1.29573, -0.07361, 0.47466

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Components

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HEAT-LABILE ENTEROTOXIN IIB, B ... , 2 types, 5 molecules DEHFG

#1: Protein HEAT-LABILE ENTEROTOXIN IIB, B CHAIN


Mass: 10794.190 Da / Num. of mol.: 3 / Fragment: RESIDUES 24-122
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: HB101 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P43529
#2: Protein HEAT-LABILE ENTEROTOXIN IIB, B CHAIN


Mass: 10778.190 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: HB101 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P43529

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Sugars , 2 types, 5 molecules

#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a3-b2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
#5: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 593 molecules

#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 589 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTERMINAL GLUTAMATE WAS CLEAVED IN SOME CHAINS. OXIDATION WAS OBSERVED IN METHIONINE69. THE ...TERMINAL GLUTAMATE WAS CLEAVED IN SOME CHAINS. OXIDATION WAS OBSERVED IN METHIONINE69. THE NUMBERING CORRESPONDS TO ONE OF THE MATURE PROTEIN (NO PEPTIDE SIGNAL).

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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: 2.9 Å3/Da / Density % sol: 57.7 % / Description: NONE
Crystal growpH: 6 / Details: 20% PEG3350, 0.2M KCL, 0.1M NA2CO3, pH 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: May 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.72→48.56 Å / Num. obs: 54271 / % possible obs: 98.4 % / Observed criterion σ(I): 3 / Redundancy: 5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.1
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TII

1tii


Resolution: 1.72→46.33 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.29 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19659 2713 5 %RANDOM
Rwork0.17106 ---
obs0.1723 51509 98.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.705 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2---1.1 Å20 Å2
3---0.86 Å2
Refinement stepCycle: LAST / Resolution: 1.72→46.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3713 0 142 589 4444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.023971
X-RAY DIFFRACTIONr_bond_other_d0.0110.023684
X-RAY DIFFRACTIONr_angle_refined_deg1.7141.9785390
X-RAY DIFFRACTIONr_angle_other_deg2.15838501
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7995498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.64924.586157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.88615645
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6161525
X-RAY DIFFRACTIONr_chiral_restr0.0970.2634
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024419
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02850
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5521.5041989
X-RAY DIFFRACTIONr_mcbond_other1.551.5041988
X-RAY DIFFRACTIONr_mcangle_it2.3042.2472488
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4911.8551982
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.72→1.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 186 -
Rwork0.262 3677 -
obs--96.36 %

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