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- PDB-3pa8: Structure of the C. difficile TcdB cysteine protease domain in co... -

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Basic information

Entry
Database: PDB / ID: 3pa8
TitleStructure of the C. difficile TcdB cysteine protease domain in complex with a peptide inhibitor
ComponentsToxin B
KeywordsTOXIN/peptide Inhibitor / Clan CD cysteine protease / protease / TOXIN / TOXIN-peptide Inhibitor complex
Function / homology
Function and homology information


host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / host cell endosome membrane / peptidase activity / toxin activity / lipid binding / host cell plasma membrane / proteolysis / extracellular region ...host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / host cell endosome membrane / peptidase activity / toxin activity / lipid binding / host cell plasma membrane / proteolysis / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
MARTX cysteine protease (CPD) domain / TcdA/TcdB toxin, N-terminal helical domain / TcdB toxin N-terminal helical domain / Dermonecrotic/RTX toxin, membrane localization domain / TcdA/TcdB toxin, catalytic glycosyltransferase domain / Membrane Localization 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 / TcdA/TcdB toxin, N-terminal helical domain / TcdB toxin N-terminal helical domain / Dermonecrotic/RTX toxin, membrane localization domain / TcdA/TcdB toxin, catalytic glycosyltransferase domain / Membrane Localization 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
N-ACETYLGLYCYL-N-[(3S)-1-HYDROXY-5-METHYL-2-OXOHEXAN-3-YL]-L-SERINAMIDE / Chem-621 / INOSITOL HEXAKISPHOSPHATE / Toxin B
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLupardus, P.J. / Garcia, K.C.
CitationJournal: Chem.Biol. / Year: 2010
Title: Rational design of inhibitors and activity-based probes targeting Clostridium difficile virulence factor TcdB.
Authors: Puri, A.W. / Lupardus, P.J. / Deu, E. / Albrow, V.E. / Garcia, K.C. / Bogyo, M. / Shen, A.
History
DepositionOct 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Dec 12, 2012Group: Other
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_conn_type / 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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_conn_type.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
A: Toxin B
B: Toxin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8789
Polymers57,8092
Non-polymers2,0697
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-68 kcal/mol
Surface area20900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.310, 45.480, 87.230
Angle α, β, γ (deg.)90.00, 103.53, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-339-

HOH

21B-375-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 293 molecules

#2: Chemical ChemComp-621 / N-acetylglycyl-N-[(3S)-1-hydroxy-5-methyl-2-oxohexan-3-yl]-L-serinamide


Type: Peptide-like / Class: Inhibitor / Mass: 331.365 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H25N3O6
References: N-ACETYLGLYCYL-N-[(3S)-1-HYDROXY-5-METHYL-2-OXOHEXAN-3-YL]-L-SERINAMIDE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTHE STARTING PEPTIDE INHIBITOR IS ACE-GLY-SER-LEU ACYL-OXY-METHYL-KETONE. UPON REACTION IT FORMS ...THE STARTING PEPTIDE INHIBITOR IS ACE-GLY-SER-LEU ACYL-OXY-METHYL-KETONE. UPON REACTION IT FORMS COVALENT BOND THROUGH CAC ATOM OF THE 621 INHIBITOR TO CYS 155 OF THE PROTEIN

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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: 2.14 Å3/Da / Density % sol: 42.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M Tris HCl pH 8.0, 30% PEG2000 MME, 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→50 Å / Num. obs: 33449 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 28.2 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 9.2
Reflection shellResolution: 2→2.11 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 2.9 / Num. unique all: 4808 / % possible all: 100

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3HO6

3ho6


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 9.154 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23282 1692 5.1 %RANDOM
Rwork0.18504 ---
obs0.18759 31754 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.055 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20.6 Å2
2--1.47 Å20 Å2
3----0.97 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3886 0 119 286 4291
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224071
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3042.0045511
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5235485
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.58925.946185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97815752
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3141512
X-RAY DIFFRACTIONr_chiral_restr0.0760.2615
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212973
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_it0.561.52439
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.07623964
X-RAY DIFFRACTIONr_scbond_it1.66731632
X-RAY DIFFRACTIONr_scangle_it2.7194.51547
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 101 -
Rwork0.247 2328 -
obs--99.92 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4985-0.22240.37251.0178-0.26771.7819-0.0316-0.10520.0689-0.08460.02180.02730.0218-0.0850.00980.0578-0.04320.00130.06990.01770.044120.994111.394623.7716
22.0130.10090.68111.2686-0.38682.4315-0.07410.19650.1763-0.0124-0.0398-0.0109-0.03760.20350.11380.0537-0.02840.0060.07590.06220.07552.077518.250819.3863
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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