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- PDB-2wv6: Crystal structure of the cholera toxin-like B-subunit from Citrob... -

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Basic information

Entry
Database: PDB / ID: 2wv6
TitleCrystal structure of the cholera toxin-like B-subunit from Citrobacter freundii to 1.9 angstrom
ComponentsCFXB
KeywordsTOXIN / LECTIN / B SUBUNIT / CHOLERA TOXIN-LIKE
Function / homologyHeat-labile enterotoxin, B chain / Heat-labile enterotoxin beta chain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / extracellular region / Mainly Beta / CFXB
Function and homology information
Biological speciesCITROBACTER FREUNDII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.895 Å
AuthorsJansson, L. / Lebens, M. / Imberty, A. / Varrot, A. / Teneberg, S.
CitationJournal: Biochimie / Year: 2010
Title: Carbohydrate Binding Specificities and Crystal Structure of the Cholera Toxin-Like B-Subunit from Citrobacter Freundii.
Authors: Jansson, L. / Angstrom, J. / Lebens, M. / Imberty, A. / Varrot, A. / Teneberg, S.
History
DepositionOct 15, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
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: CFXB
E: CFXB
F: CFXB
G: CFXB
H: CFXB
I: CFXB
J: CFXB
K: CFXB
L: CFXB
M: CFXB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,94722
Polymers116,96210
Non-polymers98512
Water9,224512
1
I: CFXB
J: CFXB
K: CFXB
L: CFXB
M: CFXB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,06612
Polymers58,4815
Non-polymers5857
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12190 Å2
ΔGint-53.3 kcal/mol
Surface area18900 Å2
MethodPISA
2
D: CFXB
E: CFXB
F: CFXB
G: CFXB
H: CFXB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,88210
Polymers58,4815
Non-polymers4005
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11550 Å2
ΔGint-48.4 kcal/mol
Surface area19680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.050, 100.940, 83.270
Angle α, β, γ (deg.)90.00, 122.24, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11G-2039-

HOH

21L-2016-

HOH

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Components

#1: Protein
CFXB / AB5 TOXIN


Mass: 11696.230 Da / Num. of mol.: 10 / Fragment: B SUBUNIT, RESIDUES 23-125
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CITROBACTER FREUNDII (bacteria) / Plasmid: PML-HCFXBTAC / Production host: VIBRIO CHOLERAE (bacteria) / Strain (production host): JS1569 / References: UniProt: Q8GAV5
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 512 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE FIRST 22 AMINO ACID CORRESPOND TO THE PEPTIDE SIGNAL. OUR NUMBERING START AT THE FIRST RESIDUE ...THE FIRST 22 AMINO ACID CORRESPOND TO THE PEPTIDE SIGNAL. OUR NUMBERING START AT THE FIRST RESIDUE FROM THE MATURE PROTEIN EQUAL TO NUMBER 23 IN THE DEPOSITED SEQUENCE

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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: 1.98 Å3/Da / Density % sol: 37.95 % / Description: NONE
Crystal growpH: 4.6
Details: 10% PEG 6K, 1 M LITHIUM CHLORIDE AND 100 MM SODIUM ACETATE PH 4.6. 20% GLYECROL WERE ADDED AS CRYOPROTECTANT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 4, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.895→43.9 Å / Num. obs: 71465 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.1
Reflection shellResolution: 1.89→2 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.9 / % possible all: 89.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EFX

3efx


Resolution: 1.895→40.9 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.003 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21121 3600 5 %RANDOM
Rwork0.17364 ---
obs0.17551 67864 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.686 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å2-0.55 Å2
2---0.54 Å20 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.895→40.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7427 0 64 512 8003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0227682
X-RAY DIFFRACTIONr_bond_other_d0.0070.025187
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.9610388
X-RAY DIFFRACTIONr_angle_other_deg0.9453.00312722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3985941
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.04325.176340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.075151386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2581533
X-RAY DIFFRACTIONr_chiral_restr0.0940.21202
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028279
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021436
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_it1.0751.54708
X-RAY DIFFRACTIONr_mcbond_other0.2531.51875
X-RAY DIFFRACTIONr_mcangle_it1.96127641
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7132974
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4294.52733
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: 1.895→1.944 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 230 -
Rwork0.226 4108 -
obs--81.24 %

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