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- PDB-4fnf: LT-IIB-B5 S74D mutant -

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Basic information

Entry
Database: PDB / ID: 4fnf
TitleLT-IIB-B5 S74D mutant
ComponentsHeat-labile enterotoxin IIB, B chain
KeywordsTOXIN / B pentamer of LT-IIb
Function / homology
Function and homology information


perturbation of signal transduction in another organism / 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
ACETATE ION / Heat-labile enterotoxin IIB, B chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsCody, V.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structure-activity correlations of variant forms of the B pentamer of Escherichia coli type II heat-labile enterotoxin LT-IIb with Toll-like receptor 2 binding.
Authors: Cody, V. / Pace, J. / Nawar, H.F. / King-Lyons, N. / Liang, S. / Connell, T.D. / Hajishengallis, G.
History
DepositionJun 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
A: Heat-labile enterotoxin IIB, B chain
B: Heat-labile enterotoxin IIB, B chain
C: Heat-labile enterotoxin IIB, B chain
I: Heat-labile enterotoxin IIB, B chain
J: Heat-labile enterotoxin IIB, B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,36120
Polymers106,77110
Non-polymers59010
Water17,330962
1
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)53,5638
Polymers53,3855
Non-polymers1773
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12480 Å2
ΔGint-97 kcal/mol
Surface area18500 Å2
MethodPISA
2
A: Heat-labile enterotoxin IIB, B chain
B: Heat-labile enterotoxin IIB, B chain
C: Heat-labile enterotoxin IIB, B chain
I: Heat-labile enterotoxin IIB, B chain
J: Heat-labile enterotoxin IIB, B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,79912
Polymers53,3855
Non-polymers4137
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12940 Å2
ΔGint-99 kcal/mol
Surface area18240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.924, 70.648, 121.630
Angle α, β, γ (deg.)90.00, 117.29, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21A
12E
22B
13F
23C
14G
24I
15H
25J

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 4 / Auth seq-ID: 1 - 98 / Label seq-ID: 1 - 98

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11DA
21AF
12EB
22BG
13FC
23CH
14GD
24II
15HE
25JJ

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: Protein
Heat-labile enterotoxin IIB, B chain / LT-IIB


Mass: 10677.086 Da / Num. of mol.: 10 / Fragment: UNP Residues 24-121 / Mutation: S74D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: DH5aF'Kan / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: P43529
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 962 / Source method: isolated from a natural source / Formula: H2O

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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: 2.54 Å3/Da / Density % sol: 51.53 %
Crystal growTemperature: 287 K / Method: microbatch under oil / pH: 8
Details: 20% PEG400, 100 mM K2HPO4, 100 mM Na acetate, pH 5.0, microbatch under oil, temperature 287K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.975 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 21, 2009 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.6→45.6 Å / Num. all: 69593 / Num. obs: 99371 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.06 / Net I/σ(I): 6.2
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 6.2 / Rsym value: 0.06 / % possible all: 98.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QB5

1qb5


Resolution: 1.75→30.82 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.469 / SU ML: 0.104 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.155 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.283 5226 5 %RANDOM
Rwork0.234 ---
obs0.237 99371 97 %-
all-99371 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.284 Å
Refinement stepCycle: LAST / Resolution: 1.75→30.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7420 0 40 962 8422
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0227865
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3751.9510658
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.06951016
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.01824.683331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.764151333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5181553
X-RAY DIFFRACTIONr_chiral_restr0.2270.21202
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0215965
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.5041.55098
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.41528172
X-RAY DIFFRACTIONr_scbond_it3.91132767
X-RAY DIFFRACTIONr_scangle_it6.24.52486
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1D731MEDIUM POSITIONAL0.810.5
1D731MEDIUM THERMAL2.32
2E735MEDIUM POSITIONAL0.250.5
2E735MEDIUM THERMAL1.852
3F723MEDIUM POSITIONAL0.530.5
3F723MEDIUM THERMAL1.662
4G734MEDIUM POSITIONAL0.330.5
4G734MEDIUM THERMAL2.032
5H727MEDIUM POSITIONAL0.320.5
5H727MEDIUM THERMAL1.822
1D731MEDIUM POSITIONAL0.810.5
1D735MEDIUM POSITIONAL0.250.5
1D723MEDIUM POSITIONAL0.530.5
1D734MEDIUM POSITIONAL0.330.5
1D727MEDIUM POSITIONAL0.320.5
1D731MEDIUM THERMAL2.32
1D735MEDIUM THERMAL1.852
1D723MEDIUM THERMAL1.662
1D734MEDIUM THERMAL2.032
1D727MEDIUM THERMAL1.822
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.528 378 -
Rwork0.491 6720 -
obs--89.09 %

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