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- PDB-5umi: Clostridium difficile TcdA-CROPs bound to PA50 Fab -

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Basic information

Entry
Database: PDB / ID: 5umi
TitleClostridium difficile TcdA-CROPs bound to PA50 Fab
Components
  • PA50 Fab Heavy chain
  • PA50 Fab Light chain
  • Toxin A
KeywordsTOXIN/IMMUNE SYSTEM / toxin antibody / TOXIN-IMMUNE SYSTEM complex
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
Cholin Binding / left handed beta-beta-3-solenoid / 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 ...Cholin Binding / left handed beta-beta-3-solenoid / 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 / Ribbon / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesClostridioides difficile (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.23 Å
AuthorsKroh, H.K. / Chandrasekaran, R. / Rosenthal, K. / Woods, R. / Jin, X. / Ohi, M.D. / Nyborg, A.C. / Rainey, G.J. / Warrener, P. / Spiller, B.W. / Lacy, D.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI095755 United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Use of a neutralizing antibody helps identify structural features critical for binding of Clostridium difficile toxin TcdA to the host cell surface.
Authors: Kroh, H.K. / Chandrasekaran, R. / Rosenthal, K. / Woods, R. / Jin, X. / Ohi, M.D. / Nyborg, A.C. / Rainey, G.J. / Warrener, P. / Spiller, B.W. / Lacy, D.B.
History
DepositionJan 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_audit_support.funding_organization
Revision 1.2Sep 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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
C: Toxin A
L: PA50 Fab Light chain
H: PA50 Fab Heavy chain
B: PA50 Fab Light chain
A: PA50 Fab Heavy chain


Theoretical massNumber of molelcules
Total (without water)123,9715
Polymers123,9715
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.685, 77.330, 97.781
Angle α, β, γ (deg.)90.00, 90.91, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein Toxin A


Mass: 30318.670 Da / Num. of mol.: 1 / Fragment: UNP residues 2461-2710
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: toxA, tcdA / Plasmid: pHIS1622 / Production host: Bacillus megaterium (bacteria)
References: UniProt: P16154, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Antibody PA50 Fab Light chain


Mass: 22999.506 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody PA50 Fab Heavy chain


Mass: 23826.764 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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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: 2.86 Å3/Da / Density % sol: 56.94 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Tris pH 7.5 0.6 M calcium chloride 19% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Aug 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 3.2→48.884 Å / Num. obs: 21838 / % possible obs: 96.3 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.142 / Net I/σ(I): 8.5
Reflection shellResolution: 3.2→3.23 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.64 / % possible all: 83.6

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G7C, 3L5X

2g7c

3l5x


Resolution: 3.23→48.884 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31
RfactorNum. reflection% reflection
Rfree0.2896 1116 5.18 %
Rwork0.27 --
obs0.271 21558 95.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.23→48.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6855 0 0 0 6855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037035
X-RAY DIFFRACTIONf_angle_d0.6069562
X-RAY DIFFRACTIONf_dihedral_angle_d13.8754120
X-RAY DIFFRACTIONf_chiral_restr0.0461028
X-RAY DIFFRACTIONf_plane_restr0.0051232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.23-3.3770.41341070.34782086X-RAY DIFFRACTION78
3.377-3.5550.33641420.32382199X-RAY DIFFRACTION84
3.555-3.77760.28741680.3032645X-RAY DIFFRACTION100
3.7776-4.06920.26151340.27322694X-RAY DIFFRACTION100
4.0692-4.47840.27161510.23932661X-RAY DIFFRACTION100
4.4784-5.12590.25331390.23312673X-RAY DIFFRACTION100
5.1259-6.45570.32011500.26332706X-RAY DIFFRACTION100
6.4557-48.88970.27691250.26812778X-RAY DIFFRACTION99
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)
17.20120.7357-3.3150.9642.00117.6532-0.1637-0.5572-0.8296-0.0834-0.3632-0.0690.460.72740.71790.60030.0898-0.05020.7863-0.01141.680352.6404-122.221384.6152
21.669-1.9786-1.96769.00840.82562.4569-0.01190.2797-0.7112-0.0337-0.12-0.63930.21120.1230.09680.59780.0716-0.22840.5359-0.15041.069835.9238-107.504182.7566
33.68383.08280.45489.123-3.31561.636-0.11170.8072-0.3472-0.37570.6026-0.73460.2324-0.1627-0.33390.53240.09890.14570.9936-0.2360.485139.8784-75.769967.3409
49.31164.31110.10396.7217-4.56354.4969-0.36120.9169-0.2128-0.2703-0.3406-0.081-1.10911.70890.47981.0352-0.076-0.21621.015-0.26930.845357.2163-57.952571.957
53.52620.6271-0.3542.93042.03797.02990.3092-0.3908-1.10970.171-0.0810.19540.7918-0.9017-0.10450.522-0.0831-0.1240.57320.15571.013510.9761-105.316102.1395
61.7852.26680.89163.42460.34644.67880.0247-0.1056-0.3745-0.21410.16220.0573-0.4458-0.41680.07880.4963-0.1428-0.13780.63570.03161.0613.7206-99.302698.6564
74.19553.0954-1.04242.3707-1.27252.0810.2447-0.41771.63731.0301-0.36822.0117-0.5678-0.61530.16110.66130.08770.0091.1831-0.19261.122-3.6745-73.3401115.6545
83.91591.1044-2.19785.231-0.80691.193-0.79440.6467-0.0033-0.45630.8114-0.1121-0.5944-0.59490.04160.794-0.038-0.31531.0072-0.24040.9883-7.7117-81.1926107.7578
92.0789-1.4577-1.61117.11916.11047.8915-0.0412-1.11130.8144-0.49710.17560.5099-2.2931-2.3378-0.21170.78450.13930.00191.80350.07511.021-5.8026-71.0347103.6203
105.0196-1.5905-2.09888.8682.5288.7627-0.0701-4.2792-0.11171.36410.6337-0.12421.3952-0.2327-0.84610.6248-0.231-0.13892.12660.04280.93460.4306-90.46116.0365
110.3602-0.41050.55171.11310.74723.4640.4672-0.38261.2898-0.5174-0.65970.6412-0.6287-0.34370.01830.68010.15690.05170.9723-0.221.5917-9.9168-68.6506110.5366
126.6981-1.48261.0965.704-2.29694.11310.404-0.4959-0.237-0.0784-0.23060.20860.0957-0.0008-0.21710.427-0.1146-0.03680.3718-0.05110.580330.4364-90.407298.9716
134.2539-0.051.46573.30962.91482.86170.3465-0.0626-0.3943-0.16180.1003-0.17870.46870.2569-0.20440.4371-0.1216-0.05080.41530.02680.765727.9937-91.6963100.9916
148.1133-1.067-5.30213.71761.71583.83120.772-0.93730.07460.4305-0.37050.1085-0.3417-0.1785-0.42320.79250.03120.08191.2018-0.33390.75636.1148-72.4587115.9431
158.01550.5015-7.35216.0537-1.99517.51770.0195-1.66150.59871.0641-0.7206-0.0276-0.7246-0.1606-0.16790.4401-0.00240.03651.1842-0.37160.8918.0312-75.7759116.9154
168.99312.0442-4.08941.7552-2.8224.4040.2262-2.528-0.43370.5772-0.8455-0.4131-0.33012.9483-0.42451.0821-0.2852-0.34712.0398-0.35491.16449.6003-72.3049126.4903
177.4153-1.62124.9150.2811-1.06763.1805-2.22161.87540.7125-0.08420.38040.2791-1.5796-0.06671.37431.4129-0.4588-0.14021.95930.15581.122823.4122-58.979936.9676
183.5469-0.169-1.89616.989-1.35835.04780.0678-0.40670.7126-2.27160.6825-0.27270.81650.2697-0.14631.2345-0.6353-0.04112.3280.12860.970829.947-68.697443.6176
192.64924.21753.54727.42325.33595.4517-0.68180.180.1184-1.8180.95851.962-0.1249-1.0558-0.15121.0154-0.401-0.04521.83630.29651.004419.093-61.542750.2191
201.76620.2825-1.30344.9146-0.470.9454-0.56871.83110.3431-0.4053-0.21861.04560.78080.37250.55891.3435-0.4229-0.25312.12090.05170.868118.9611-68.481543.5515
211.96342.11940.08693.22732.13394.4182-1.00351.52220.6511.21571.53491.1431.3390.259-1.39131.7534-0.6144-0.73362.24940.89391.543710.5435-57.047640.2939
220.65310.0122-0.87740.07750.12691.3727-0.34861.8810.1004-0.1663-0.03280.23441.2795-0.5536-1.00781.4963-0.7445-0.4242.16830.29790.324926.5948-59.797248.1045
239.49964.25240.98527.5463-2.41333.3852-1.28280.53311.2119-0.33261.40420.8733-0.3405-0.15340.27781.04460.3077-0.13161.31550.06820.69623.2409-52.963367.6757
248.75983.5926-0.18258.0973-1.55954.8903-10.8716-0.1074-0.56171.31670.10860.1045-0.9823-0.2520.82760.1444-0.11470.9470.05950.657333.6571-56.516461.5715
251.5572.38230.18657.112-0.4624.2924-0.7240.28180.920.04290.55621.1467-0.7201-0.5144-0.14430.84020.3233-0.01041.25150.37191.064927.0341-53.254763.942
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 2461 through 2493 )
2X-RAY DIFFRACTION2chain 'C' and (resid 2494 through 2573 )
3X-RAY DIFFRACTION3chain 'C' and (resid 2574 through 2687 )
4X-RAY DIFFRACTION4chain 'C' and (resid 2688 through 2705 )
5X-RAY DIFFRACTION5chain 'L' and (resid 1 through 84 )
6X-RAY DIFFRACTION6chain 'L' and (resid 85 through 103 )
7X-RAY DIFFRACTION7chain 'L' and (resid 104 through 134 )
8X-RAY DIFFRACTION8chain 'L' and (resid 135 through 147 )
9X-RAY DIFFRACTION9chain 'L' and (resid 148 through 160 )
10X-RAY DIFFRACTION10chain 'L' and (resid 161 through 171 )
11X-RAY DIFFRACTION11chain 'L' and (resid 172 through 210 )
12X-RAY DIFFRACTION12chain 'H' and (resid 2 through 73 )
13X-RAY DIFFRACTION13chain 'H' and (resid 74 through 111 )
14X-RAY DIFFRACTION14chain 'H' and (resid 112 through 140 )
15X-RAY DIFFRACTION15chain 'H' and (resid 141 through 189 )
16X-RAY DIFFRACTION16chain 'H' and (resid 190 through 214 )
17X-RAY DIFFRACTION17chain 'B' and (resid 2 through 18 )
18X-RAY DIFFRACTION18chain 'B' and (resid 19 through 32 )
19X-RAY DIFFRACTION19chain 'B' and (resid 33 through 52 )
20X-RAY DIFFRACTION20chain 'B' and (resid 53 through 74 )
21X-RAY DIFFRACTION21chain 'B' and (resid 75 through 83 )
22X-RAY DIFFRACTION22chain 'B' and (resid 84 through 102 )
23X-RAY DIFFRACTION23chain 'A' and (resid 2 through 36 )
24X-RAY DIFFRACTION24chain 'A' and (resid 37 through 67 )
25X-RAY DIFFRACTION25chain 'A' and (resid 68 through 118 )

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