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- PDB-3pee: Structure of the C. difficile TcdB cysteine protease domain -

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Basic information

Entry
Database: PDB / ID: 3pee
TitleStructure of the C. difficile TcdB cysteine protease domain
ComponentsToxin B
KeywordsTOXIN / Clan CD cysteine protease / protease / inositol hexakisphosphate
Function / homology
Function and homology information


host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / cysteine-type peptidase activity / host cell endosome membrane / toxin activity / lipid binding / host cell plasma membrane / proteolysis / extracellular region ...host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / cysteine-type peptidase activity / host cell endosome membrane / toxin activity / lipid binding / host cell plasma membrane / proteolysis / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
MARTX cysteine protease (CPD) domain / Dermonecrotic/RTX toxin, membrane localization domain / TcdA/TcdB toxin, N-terminal helical domain / TcdB toxin N-terminal helical domain / Membrane Localization 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 ...MARTX cysteine protease (CPD) domain / Dermonecrotic/RTX toxin, membrane localization domain / TcdA/TcdB toxin, N-terminal helical domain / TcdB toxin N-terminal helical domain / Membrane Localization 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 B
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLupardus, P.J. / Garcia, K.C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Defining an allosteric circuit in the cysteine protease domain of Clostridium difficile toxins.
Authors: Shen, A. / Lupardus, P.J. / Gersch, M.M. / Puri, A.W. / Albrow, V.E. / Garcia, K.C. / Bogyo, M.
History
DepositionOct 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 31, 2011Group: Database references
Revision 1.3Oct 14, 2020Group: Derived calculations / Structure summary
Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _pdbx_struct_conn_angle.ptnr1_auth_asym_id ..._chem_comp.pdbx_synonyms / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
B: Toxin B
A: Toxin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1695
Polymers57,8092
Non-polymers1,3603
Water3,927218
1
A: Toxin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5642
Polymers28,9041
Non-polymers6601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Toxin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6053
Polymers28,9041
Non-polymers7002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.110, 45.710, 87.350
Angle α, β, γ (deg.)90.00, 103.48, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-289-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25
16
26
17
27
18
28

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and resseq 19:44
211chain B and resseq 19:44
112chain A and resseq 89:159
212chain B and resseq 89:159
113chain A and resseq 78:85
213chain B and resseq 78:85
114chain A and resseq 167:197
214chain B and resseq 167:197
115chain A and resseq 202:212
215chain B and resseq 202:212
116chain A and resseq 219:236
216chain B and resseq 219:236
117chain A and resseq 246:254
217chain B and resseq 246:254
118chain A and resseq 50:76
218chain B and resseq 50:76

NCS ensembles :
ID
1
2
3
4
5
6
7
8

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Components

#1: Protein Toxin B


Mass: 28904.412 Da / Num. of mol.: 2 / Fragment: UNP residues 544-797
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: CD0660, tcdB / Plasmid: pet22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q189K3
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.15 Å3/Da / Density % sol: 42.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M Tris HCl pH 8.0, 30% PEG2000MME, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 28295 / % possible obs: 97.6 % / Redundancy: 3.2 % / Biso Wilson estimate: 36.6 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 8.4
Reflection shellResolution: 2.1→2.22 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.8 / % possible all: 91.8

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3HO6

3ho6


Resolution: 2.1→39.657 Å / SU ML: 0.31 / σ(F): 0.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2403 1337 5.08 %RANDOM
Rwork0.1917 ---
obs0.1941 26305 90.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.829 Å2 / ksol: 0.323 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.3059 Å20 Å20.486 Å2
2--0.6163 Å2-0 Å2
3---3.6896 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3854 0 73 218 4145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083993
X-RAY DIFFRACTIONf_angle_d1.3085413
X-RAY DIFFRACTIONf_dihedral_angle_d16.21516
X-RAY DIFFRACTIONf_chiral_restr0.081608
X-RAY DIFFRACTIONf_plane_restr0.004679
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A203X-RAY DIFFRACTIONPOSITIONAL
12B203X-RAY DIFFRACTIONPOSITIONAL0.04
21A546X-RAY DIFFRACTIONPOSITIONAL
22B546X-RAY DIFFRACTIONPOSITIONAL0.062
31A57X-RAY DIFFRACTIONPOSITIONAL
32B57X-RAY DIFFRACTIONPOSITIONAL0.029
41A236X-RAY DIFFRACTIONPOSITIONAL
42B236X-RAY DIFFRACTIONPOSITIONAL0.042
51A93X-RAY DIFFRACTIONPOSITIONAL
52B93X-RAY DIFFRACTIONPOSITIONAL0.042
61A146X-RAY DIFFRACTIONPOSITIONAL
62B146X-RAY DIFFRACTIONPOSITIONAL0.044
71A47X-RAY DIFFRACTIONPOSITIONAL
72B47X-RAY DIFFRACTIONPOSITIONAL0.1
81A214X-RAY DIFFRACTIONPOSITIONAL
82B214X-RAY DIFFRACTIONPOSITIONAL0.045
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.17820.31281460.2571999X-RAY DIFFRACTION74
2.1782-2.26540.34291150.24712184X-RAY DIFFRACTION81
2.2654-2.36850.30031080.23912274X-RAY DIFFRACTION84
2.3685-2.49330.28971230.23422420X-RAY DIFFRACTION88
2.4933-2.64950.30721390.22772498X-RAY DIFFRACTION92
2.6495-2.8540.30751320.2312620X-RAY DIFFRACTION95
2.854-3.14120.27251470.22272626X-RAY DIFFRACTION97
3.1412-3.59540.21411410.18292747X-RAY DIFFRACTION99
3.5954-4.52880.20431450.14082754X-RAY DIFFRACTION99
4.5288-39.66360.17291410.16432846X-RAY DIFFRACTION100

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