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- PDB-3zjx: Clostridium perfringens epsilon toxin mutant H149A bound to octyl... -

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Basic information

Entry
Database: PDB / ID: 3zjx
TitleClostridium perfringens epsilon toxin mutant H149A bound to octyl glucoside
ComponentsEPSILON-TOXIN
KeywordsTOXIN / PORE FORMING TOXIN / ENTEROTOXEMIA / AEROLYSIN FAMILY
Function / homology
Function and homology information


Dihydrodipicolinate Reductase; domain 2 - #60 / Epsilon toxin / Proaerolysin, chain A, domain 3 / Aerolysin-like toxin / Clostridium epsilon toxin ETX/Bacillus mosquitocidal toxin MTX2 / Proaerolysin; Chain A, domain 3 / Dihydrodipicolinate Reductase; domain 2 / Beta Complex / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Epsilon-toxin
Similarity search - Component
Biological speciesCLOSTRIDIUM PERFRINGENS D (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBokori-Brown, M. / Kokkinidou, M.C. / Savva, C.G. / Fernandes da Costa, S.P. / Naylor, C.E. / Cole, A.R. / Basak, A.K. / Titball, R.W.
CitationJournal: Protein Sci. / Year: 2013
Title: Clostridium Perfringens Epsilon Toxin H149A Mutant as a Platform for Receptor Binding Studies.
Authors: Bokori-Brown, M. / Kokkinidou, M.C. / Savva, C.G. / Da Costa, S.P. / Naylor, C.E. / Cole, A.R. / Moss, D.S. / Basak, A.K. / Titball, R.W.
History
DepositionJan 20, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Database references
Revision 1.2Apr 1, 2015Group: Data collection
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 20, 2023Group: 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_ncs_dom_lim / struct_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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_sheet.number_strands
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EPSILON-TOXIN
B: EPSILON-TOXIN
C: EPSILON-TOXIN
D: EPSILON-TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,88812
Polymers128,3394
Non-polymers1,5498
Water8,269459
1
A: EPSILON-TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4723
Polymers32,0851
Non-polymers3872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: EPSILON-TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4723
Polymers32,0851
Non-polymers3872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: EPSILON-TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4723
Polymers32,0851
Non-polymers3872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: EPSILON-TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4723
Polymers32,0851
Non-polymers3872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.709, 123.709, 127.314
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11C-2109-

HOH

21D-2100-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYAA14 - 2943 - 287
21GLYGLYBB14 - 2943 - 287
12GLYGLYAA14 - 2943 - 287
22GLYGLYCC14 - 2943 - 287
13ILEILEAA14 - 2953 - 288
23ILEILEDD14 - 2953 - 288

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(-0.9998, 0.0218, 0.0002), (-0.0218, -0.9998, 0.0023), (0.0003, 0.0023, 1)-63.38, 178.4045, 63.4298
2given(-0.9998, 0.0218, 0.0002), (-0.0218, -0.9998, 0.0023), (0.0003, 0.0023, 1)-63.38, 178.4045, 63.4298
3given(0.4802, 0.8772, -0.0008), (0.8772, -0.4802, -0.0012), (-0.0015, -0.0001, -1)-63.4127, 178.6186, 170.6061

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Components

#1: Protein
EPSILON-TOXIN


Mass: 32084.779 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM PERFRINGENS D (bacteria) / Strain: NCTC 8346 / Plasmid: PHIS PARALLEL II / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E7D8R1
#2: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 459 / 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: 4.39 Å3/Da / Density % sol: 72 % / Description: NONE
Crystal growDetails: 0.85 M AMMONIUM DIHYDROGEN PHOSPHATE AND 0.5% (W/V) OCTYLGLUCOSIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.373
11-K, -H, -L20.135
11K, H, -L30.361
11-h,-k,l40.131
ReflectionResolution: 2.4→21.56 Å / Num. obs: 85072 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.3
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UYJ

1uyj


Resolution: 2.4→21.56 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.01 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.27543 4258 5 %RANDOM
Rwork0.2467 ---
obs0.24817 80521 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.565 Å2
Baniso -1Baniso -2Baniso -3
1-11.39 Å20 Å20 Å2
2--11.39 Å20 Å2
3----22.78 Å2
Refinement stepCycle: LAST / Resolution: 2.4→21.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8443 0 100 459 9002
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.028685
X-RAY DIFFRACTIONr_bond_other_d0.0030.027971
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.94911840
X-RAY DIFFRACTIONr_angle_other_deg0.908318324
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.23351094
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.326.231390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.696151376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3911520
X-RAY DIFFRACTIONr_chiral_restr0.080.21400
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219974
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021902
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_it2.8625.2774397
X-RAY DIFFRACTIONr_mcbond_other2.8625.2764396
X-RAY DIFFRACTIONr_mcangle_it4.3587.8975481
X-RAY DIFFRACTIONr_mcangle_other4.3587.8975482
X-RAY DIFFRACTIONr_scbond_it3.1395.5554288
X-RAY DIFFRACTIONr_scbond_other3.1355.5534273
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8178.2176335
X-RAY DIFFRACTIONr_long_range_B_refined7.26342.3879241
X-RAY DIFFRACTIONr_long_range_B_other7.26242.3889242
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A144430.07
12B144430.07
21A145090.08
22C145090.08
31A141170.09
32D141170.09
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.632 346 -
Rwork0.708 5890 -
obs--98.66 %

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