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- PDB-3ho6: Structure-function analysis of inositol hexakisphosphate-induced ... -

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Basic information

Entry
Database: PDB / ID: 3ho6
TitleStructure-function analysis of inositol hexakisphosphate-induced autoprocessing in clostridium difficile toxin A
ComponentsToxin A
KeywordsTOXIN / inositol phosphate / Enterotoxin
Function / homology
Function and homology information


host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / cysteine-type peptidase activity / host cell endosome membrane / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lipid binding / host cell plasma membrane / proteolysis ...host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / cysteine-type peptidase activity / host cell endosome membrane / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lipid binding / host cell plasma membrane / proteolysis / extracellular region / membrane / metal ion binding
Similarity search - Function
MARTX cysteine protease (CPD) domain / TcdA/TcdB toxin, N-terminal helical domain / TcdB toxin N-terminal helical domain / TcdA/TcdB toxin, catalytic glycosyltransferase domain / TcdA/TcdB catalytic glycosyltransferase domain / TcdA/TcdB toxin, pore forming domain / TcdA/TcdB pore forming domain / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily / Peptidase C80 family ...MARTX cysteine protease (CPD) domain / TcdA/TcdB toxin, N-terminal helical domain / TcdB toxin N-terminal helical domain / TcdA/TcdB toxin, catalytic glycosyltransferase domain / TcdA/TcdB catalytic glycosyltransferase domain / TcdA/TcdB toxin, pore forming domain / TcdA/TcdB pore forming domain / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily / Peptidase C80 family / CGT/MARTX cysteine protease (CPD) domain profile. / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Nucleotide-diphospho-sugar transferases / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / Toxin A
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsPruitt, R.N. / Lacy, D.B.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structure-function analysis of inositol hexakisphosphate-induced autoprocessing in Clostridium difficile toxin A.
Authors: Pruitt, R.N. / Chagot, B. / Cover, M. / Chazin, W.J. / Spiller, B. / Lacy, D.B.
History
DepositionJun 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 14, 2020Group: Derived calculations / Structure summary / Category: chem_comp / struct_site
Item: _chem_comp.pdbx_synonyms / _struct_site.pdbx_auth_asym_id ..._chem_comp.pdbx_synonyms / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Toxin A
B: Toxin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7444
Polymers60,4242
Non-polymers1,3202
Water11,674648
1
A: Toxin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8722
Polymers30,2121
Non-polymers6601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Toxin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8722
Polymers30,2121
Non-polymers6601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)141.312, 43.500, 94.692
Angle α, β, γ (deg.)90.00, 112.88, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Toxin A


Mass: 30211.922 Da / Num. of mol.: 2 / Fragment: UNP residues 543-809
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Gene: tcdA, toxA / Plasmid: pET27 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21.DE3 / References: UniProt: P16154
#2: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H18O24P6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 648 / 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: 2.22 Å3/Da / Density % sol: 44.56 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 100 mM Tris, 25-30 % PEG 8000, and 200 mM guanadinium chloride, pH 8-9, VAPOR DIFFUSION, HANGING DROP, temperature 294K
PH range: 8-9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9784 Å
DetectorDetector: CCD / Date: Nov 1, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9784 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 70828 / Num. obs: 68137 / % possible obs: 96.2 % / Observed criterion σ(I): 2.4 / Redundancy: 4.8 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.043 / Net I/σ(I): 23.5
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.268 / % possible all: 81.9

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Processing

Software
NameClassification
HKL-2000data collection
SHARPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.6→31.502 Å / SU ML: 0.55 / Isotropic thermal model: anisotropic / σ(F): 1.34 / Phase error: 22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1982 3440 5.05 %
Rwork0.1651 --
obs0.1668 68090 95.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.621 Å2 / ksol: 0.404 e/Å3
Refinement stepCycle: LAST / Resolution: 1.6→31.502 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7975 0 84 648 8707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078145
X-RAY DIFFRACTIONf_angle_d1.23414761
X-RAY DIFFRACTIONf_dihedral_angle_d14.8542180
X-RAY DIFFRACTIONf_chiral_restr0.077623
X-RAY DIFFRACTIONf_plane_restr0.0051270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.61770.3024940.23581745X-RAY DIFFRACTION65
1.6177-1.64080.27031170.22192356X-RAY DIFFRACTION88
1.6408-1.66530.21410.2162416X-RAY DIFFRACTION90
1.6653-1.69130.26261390.21222485X-RAY DIFFRACTION93
1.6913-1.7190.2241360.20282567X-RAY DIFFRACTION95
1.719-1.74860.24471290.18722599X-RAY DIFFRACTION96
1.7486-1.78040.22661350.17292578X-RAY DIFFRACTION97
1.7804-1.81470.20041480.17182625X-RAY DIFFRACTION98
1.8147-1.85170.20371380.1692603X-RAY DIFFRACTION98
1.8517-1.8920.17621290.16282655X-RAY DIFFRACTION98
1.892-1.9360.21121340.16142610X-RAY DIFFRACTION98
1.936-1.98440.21741430.16452632X-RAY DIFFRACTION98
1.9844-2.0380.22291560.1652612X-RAY DIFFRACTION98
2.038-2.0980.20131340.15972675X-RAY DIFFRACTION98
2.098-2.16570.19531450.15992643X-RAY DIFFRACTION98
2.1657-2.24310.18181650.16472630X-RAY DIFFRACTION99
2.2431-2.33290.22961290.15772656X-RAY DIFFRACTION99
2.3329-2.4390.19351490.15552672X-RAY DIFFRACTION99
2.439-2.56750.20481210.15872689X-RAY DIFFRACTION99
2.5675-2.72830.22961330.16432715X-RAY DIFFRACTION99
2.7283-2.93880.18761410.16172680X-RAY DIFFRACTION99
2.9388-3.23430.19991520.16062682X-RAY DIFFRACTION99
3.2343-3.70170.16511580.14332712X-RAY DIFFRACTION99
3.7017-4.66130.16061440.1362686X-RAY DIFFRACTION98
4.6613-31.5080.19021300.1652727X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.2182-1.1709-2.24460.58470.47740.51790.3161-0.23350.26390.249-0.25020.0059-0.1151-0.5770.02740.29870.13090.040.52770.04720.375450.80322.299918.7084
20.95030.1301-0.43730.98050.19112.22550.03210.05230.1068-0.16620.0452-0.0909-0.23130.0875-0.07820.2120.00780.03450.144900.187568.272312.868412.9951
3-0.2562-0.94940.2782.071-0.59161.5248-0.27390.0176-0.00150.61350.265-0.0237-0.4389-0.0791-0.06711.1540.42150.1990.52410.1450.531751.907114.060234.1918
40.84510.63280.27610.3981-1.19511.4331-0.13960.0075-0.1721-0.06910.08340.12530.3033-0.26390.010.212-0.0054-0.00370.1686-0.00620.204956.12991.60619.7301
5-0.4155-0.4641-0.5298-0.0193-1.1841-0.9732-0.25890.1922-0.1096-0.3913-0.2153-0.18880.5470.08320.41480.39860.10770.07240.1730.01950.256773.028-5.388117.248
60.69140.1638-0.06890.6521-0.30291.7797-0.0049-0.0751-0.11160.07750.0199-0.06320.11220.0582-0.00250.21320.04040.00920.12130.0150.167865.04485.585231.1455
70.4753-0.08620.05223.11930.06550.1504-0.0015-0.0646-0.18460.6390.0253-0.27040.21340.1244-0.0040.36540.0309-0.03950.16040.02790.217567.6562-4.891736.6464
8-0.92860.26750.38821.13370.62531.1211-0.1466-0.1977-0.1781-0.03530.07690.31670.3604-0.81130.01260.2854-0.17460.07580.52980.07830.441718.46949.067132.5847
90.5429-0.3501-0.90811.473-0.26011.7294-0.0319-0.12620.05090.17820.12240.00350.01880.049-0.08620.16770.0170.00150.25470.01350.173630.786817.97330.7095
10-1.3002-0.4126-0.96172.1201-0.50833.3709-0.07690.23370.29860.2120.40360.698-0.2688-0.8459-0.30970.16720.05470.05020.41030.09660.299721.077621.849228.4345
110.8282-0.5404-1.20291.6592-0.56872.65650.09710.27840.1092-0.04210.0780.2161-0.301-0.4481-0.15670.1870.0549-0.00840.3090.06060.252624.426524.228320.8567
121.0845-0.8873-0.08961.48230.03271.87940.39250.5517-0.2047-0.5878-0.37150.29980.4082-0.6884-0.04920.3486-0.01-0.12880.4423-0.01720.203525.408110.255.3387
132.8781-0.84211.20762.00812.85361.22050.46130.6143-0.0575-1.08250.11910.0993-0.58-0.0196-0.2440.6250.1832-0.07590.43890.17530.293723.43330.08396.4406
140.3172-0.07310.48990.9-0.6011.08540.00660.0816-0.0428-0.26050.09080.0087-0.0181-0.0694-0.07460.23860.0322-0.03250.25530.00250.167436.879911.119111.0039
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 5:10)A5 - 10
2X-RAY DIFFRACTION2(chain A and resid 11:113)A11 - 113
3X-RAY DIFFRACTION3(chain A and resid 114:117)A114 - 117
4X-RAY DIFFRACTION4(chain A and resid 118:145)A118 - 145
5X-RAY DIFFRACTION5(chain A and resid 146:150)A146 - 150
6X-RAY DIFFRACTION6(chain A and resid 151:238)A151 - 238
7X-RAY DIFFRACTION7(chain A and resid 239:259)A239 - 259
8X-RAY DIFFRACTION8(chain B and resid 6:14)B6 - 14
9X-RAY DIFFRACTION9(chain B and resid 15:62)B15 - 62
10X-RAY DIFFRACTION10(chain B and resid 63:77)B63 - 77
11X-RAY DIFFRACTION11(chain B and resid 78:157)B78 - 157
12X-RAY DIFFRACTION12(chain B and resid 158:179)B158 - 179
13X-RAY DIFFRACTION13(chain B and resid 180:192)B180 - 192
14X-RAY DIFFRACTION14(chain B and resid 193:261)B193 - 261

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