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- PDB-5t87: Crystal structure of CDI complex from Cupriavidus taiwanensis LMG... -

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Basic information

Entry
Database: PDB / ID: 5t87
TitleCrystal structure of CDI complex from Cupriavidus taiwanensis LMG 19424
Components
  • CdiA toxin
  • CdiI immunity protein
KeywordsTOXIN / Contact-dependent growth inhibition / antitoxin / immunity protein / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes / UC4CDI
Function / homology
Function and homology information


catalytic activity / toxin activity / cytoplasm
Similarity search - Function
: / Toxin CdiA-like, Filamentous hemagglutinin motif repeats / VENN motif-containing domain / Pre-toxin domain with VENN motif / Hemagglutinin repeat / Hemagglutinin repeat / Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain / TPS secretion domain / haemagglutination activity domain / ESPR domain ...: / Toxin CdiA-like, Filamentous hemagglutinin motif repeats / VENN motif-containing domain / Pre-toxin domain with VENN motif / Hemagglutinin repeat / Hemagglutinin repeat / Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain / TPS secretion domain / haemagglutination activity domain / ESPR domain / Extended Signal Peptide of Type V secretion system / Pectin lyase fold / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
Exoprotein, putative adhesin or hemolysin / HEAT repeat domain-containing protein
Similarity search - Component
Biological speciesCupriavidus taiwanensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsMichalska, K. / Joachimiak, G. / Jedrzejczak, R. / Hayes, C.S. / Goulding, C.W. / Joachimiak, A. / Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes (UC4CDI) / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115586 United States
CitationJournal: Proteins / Year: 2018
Title: Target highlights from the first post-PSI CASP experiment (CASP12, May-August 2016).
Authors: Kryshtafovych, A. / Albrecht, R. / Basle, A. / Bule, P. / Caputo, A.T. / Carvalho, A.L. / Chao, K.L. / Diskin, R. / Fidelis, K. / Fontes, C.M.G.A. / Fredslund, F. / Gilbert, H.J. / Goulding, ...Authors: Kryshtafovych, A. / Albrecht, R. / Basle, A. / Bule, P. / Caputo, A.T. / Carvalho, A.L. / Chao, K.L. / Diskin, R. / Fidelis, K. / Fontes, C.M.G.A. / Fredslund, F. / Gilbert, H.J. / Goulding, C.W. / Hartmann, M.D. / Hayes, C.S. / Herzberg, O. / Hill, J.C. / Joachimiak, A. / Kohring, G.W. / Koning, R.I. / Lo Leggio, L. / Mangiagalli, M. / Michalska, K. / Moult, J. / Najmudin, S. / Nardini, M. / Nardone, V. / Ndeh, D. / Nguyen, T.H. / Pintacuda, G. / Postel, S. / van Raaij, M.J. / Roversi, P. / Shimon, A. / Singh, A.K. / Sundberg, E.J. / Tars, K. / Zitzmann, N. / Schwede, T.
History
DepositionSep 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 8, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Feb 28, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: CdiI immunity protein
B: CdiI immunity protein
C: CdiI immunity protein
D: CdiI immunity protein
E: CdiA toxin
F: CdiA toxin
G: CdiA toxin
H: CdiA toxin


Theoretical massNumber of molelcules
Total (without water)86,3498
Polymers86,3498
Non-polymers00
Water2,594144
1
A: CdiI immunity protein
E: CdiA toxin


Theoretical massNumber of molelcules
Total (without water)21,5872
Polymers21,5872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-9 kcal/mol
Surface area8930 Å2
MethodPISA
2
B: CdiI immunity protein
F: CdiA toxin


Theoretical massNumber of molelcules
Total (without water)21,5872
Polymers21,5872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-8 kcal/mol
Surface area9410 Å2
MethodPISA
3
C: CdiI immunity protein
G: CdiA toxin


Theoretical massNumber of molelcules
Total (without water)21,5872
Polymers21,5872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-9 kcal/mol
Surface area9620 Å2
MethodPISA
4
D: CdiI immunity protein
H: CdiA toxin


Theoretical massNumber of molelcules
Total (without water)21,5872
Polymers21,5872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-10 kcal/mol
Surface area9260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.097, 107.097, 315.271
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein
CdiI immunity protein


Mass: 13100.101 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus taiwanensis (strain DSM 17343 / BCRC 17206 / CIP 107171 / LMG 19424 / R1) (bacteria)
Strain: DSM 17343 / BCRC 17206 / CIP 107171 / LMG 19424 / R1
Gene: RALTA_A1586 / Plasmid: pMCSG81 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B3R1C2
#2: Protein
CdiA toxin


Mass: 8487.235 Da / Num. of mol.: 4 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Details: The cloned fragment is longer and starts with T3228 of the original sequence, however purified complex was treated with trypsin prior to crystallization. The provided sequence corresponds to ...Details: The cloned fragment is longer and starts with T3228 of the original sequence, however purified complex was treated with trypsin prior to crystallization. The provided sequence corresponds to the most likely fragment obtained after cleavage.
Source: (gene. exp.) Cupriavidus taiwanensis (strain DSM 17343 / BCRC 17206 / CIP 107171 / LMG 19424 / R1) (bacteria)
Strain: DSM 17343 / BCRC 17206 / CIP 107171 / LMG 19424 / R1
Gene: RALTA_A1585 / Plasmid: pMCSG81 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B3R1C1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.06 Å3/Da / Density % sol: 59.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.1 M Mg acetate, 0.1 M Na acetate, 8% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791519 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 24, 2014 / Details: mirrors
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791519 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 42464 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / CC1/2: 0.894 / Rmerge(I) obs: 0.143 / Net I/σ(I): 12.84
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.693 / Mean I/σ(I) obs: 1.45 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SBC-Collectdata collection
RefinementMethod to determine structure: SAD / Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.922 / SU B: 20.794 / SU ML: 0.22 / Cross valid method: THROUGHOUT / ESU R: 0.311 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24697 1086 2.6 %RANDOM
Rwork0.21528 ---
obs0.21613 41076 98.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.62 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å20.69 Å20 Å2
2--1.37 Å20 Å2
3----4.46 Å2
Refinement stepCycle: 1 / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5814 0 0 144 5958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195974
X-RAY DIFFRACTIONr_bond_other_d0.0020.025590
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.958104
X-RAY DIFFRACTIONr_angle_other_deg0.938312803
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8195747
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.30723.344305
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.52415920
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7161563
X-RAY DIFFRACTIONr_chiral_restr0.0710.2888
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216908
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021425
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_it1.1173.4372997
X-RAY DIFFRACTIONr_mcbond_other1.1113.4362996
X-RAY DIFFRACTIONr_mcangle_it1.9315.1373741
X-RAY DIFFRACTIONr_mcangle_other1.9315.1383742
X-RAY DIFFRACTIONr_scbond_it1.2353.5792976
X-RAY DIFFRACTIONr_scbond_other1.2353.5792977
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0395.3024364
X-RAY DIFFRACTIONr_long_range_B_refined3.70826.8816594
X-RAY DIFFRACTIONr_long_range_B_other3.69726.8526578
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.403→2.465 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 80 -
Rwork0.337 2706 -
obs--90.43 %
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)
11.57560.0207-1.40490.0098-0.0592.44460.0757-0.1080.10480.0044-0.0666-0.00340.24230.2187-0.00910.1729-0.0680.0280.35650.01270.0147-1.872136.079436.0504
27.6555-2.3075-1.82483.1676-0.49923.3350.10360.25560.3332-0.0894-0.0260.0504-0.4972-0.0149-0.07760.155-0.04520.0450.20280.02280.101-5.056746.991325.0759
37.87161.8301-2.58464.5789-1.21651.43550.1978-0.23830.8927-0.2131-0.12460.0883-0.1514-0.0075-0.07320.2346-0.04980.05490.231-0.0270.2438-2.557451.606431.0187
49.47060.28229.49213.83421.02489.6589-0.0799-0.1011-0.3963-0.05020.4953-0.1473-0.0976-0.0127-0.41530.227-0.0734-0.01830.1615-0.00560.106-25.719573.546150.7596
50.79350.4742-0.01610.3329-0.35332.3966-0.09230.0809-0.0969-0.05160.0512-0.06610.0145-0.03490.04110.2151-0.1338-0.01990.2249-0.00690.0623-32.017457.09342.2932
67.0906-2.67841.16371.0669-0.35960.34210.1588-0.2169-0.1349-0.038-0.00640.00140.0716-0.118-0.15230.1847-0.0516-0.0180.2140.00190.1489-38.785356.349454.4172
70.07720.0063-0.32610.18280.25241.8148-0.02820.01790.0282-0.08490.07280.04340.03710.0101-0.04450.1922-0.1459-0.01620.26120.0320.0512-26.003230.861450.6935
84.277-0.32640.0191.00050.93351.13490.0662-0.0237-0.084-0.0338-0.00660.0528-0.14850.0997-0.05970.2283-0.11710.00870.22530.01170.0677-20.747637.733259.9122
91.43694.17212.173614.92024.9034.44040.1927-0.0132-0.00180.5686-0.1244-0.05840.01550.1724-0.06830.1952-0.07830.03710.21030.00140.1784-8.27535.433164.0029
104.2886-1.48295.28722.7292-2.58686.87650.11170.261-0.1997-0.02790.06590.12950.23520.2586-0.17770.1738-0.02040.07860.2688-0.02390.0895-29.661913.090720.6232
110.68320.1504-0.5180.9465-0.65711.3697-0.03870.0889-0.03950.07460.0658-0.06670.05120.0139-0.02710.2306-0.10990.0060.23350.03050.0519-32.574620.441831.5296
126.14213.9413-1.65223.2054-2.35833.78050.1065-0.02690.54480.0966-0.01930.324-0.1839-0.3586-0.08720.1874-0.02250.03170.20680.01220.0939-43.8225.732432.0922
130.651-1.33450.12292.75-0.37454.44210.0375-0.05990.0797-0.02940.0549-0.1369-0.61140.4056-0.09240.1744-0.23120.06060.3796-0.10270.0890.849650.417748.0283
140.1520.6260.56462.70272.46972.29480.0338-0.0332-0.0047-0.0533-0.0468-0.0695-0.1051-0.01620.0130.3081-0.16690.0450.19470.03390.3114.444258.010540.2629
159.90920.76191.077519.131-16.388514.3427-0.3826-0.2339-0.7166-0.2254-0.2751-0.90090.13940.18630.65770.3003-0.1540.0330.225-0.1610.39663.536265.528248.2821
161.6989-1.67720.04825.9307-0.95421.43130.09690.0962-0.18980.0086-0.02730.6248-0.2086-0.1492-0.06960.2572-0.07710.00250.1712-0.0240.1117-34.627372.777657.3634
170.9146-0.1187-1.05112.3540.54251.2787-0.08450.1194-0.1510.0868-0.10850.13780.102-0.15190.1930.2117-0.0983-0.01190.3101-0.01470.0352-37.108767.81256.7276
183.4438-2.95231.9194.35250.63175.8383-0.12140.3142-0.20420.4831-0.01840.1908-0.0357-0.04970.13980.24520.0948-0.00840.3136-0.07050.2061-44.502774.590667.9393
191.81790.07481.183.8125-1.21971.23570.05140.0311-0.0649-0.092-0.0707-0.16750.06590.14220.01930.2173-0.0687-0.01380.23060.02470.024-19.31422.123568.3858
2013.8837-11.87413.049413.9092.537.8477-0.64260.41010.47470.917-0.15340.0840.24360.17550.7960.23380.0612-0.04210.36660.07640.1194-15.16718.971979.7694
2114.90070.4928-8.455617.0028-6.57067.1437-0.9171-0.5172-0.060.49410.7836-0.24820.36980.04860.13350.29820.1773-0.11820.26050.00090.2709-7.102416.408378.4117
222.32820.21480.76510.5991.30873.24320.00870.3602-0.1803-0.0437-0.10120.0742-0.1543-0.44020.09250.2048-0.068-0.01980.379-0.00280.0397-47.015420.515614.3202
231.3603-0.911-1.23520.61090.82941.13510.06350.2299-0.1039-0.0571-0.15250.0752-0.1082-0.15910.08910.1334-0.1474-0.03380.28920.0590.0759-48.046321.353319.6325
240.61851.7932-1.06986.3416-3.8232.31320.34590.20590.3070.5060.34681.1732-0.3013-0.1657-0.69270.44470.14590.01620.4721-0.05570.3936-62.026321.015916.0926
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 77
2X-RAY DIFFRACTION2A78 - 96
3X-RAY DIFFRACTION3A97 - 115
4X-RAY DIFFRACTION4B2 - 8
5X-RAY DIFFRACTION5B9 - 95
6X-RAY DIFFRACTION6B96 - 114
7X-RAY DIFFRACTION7C2 - 57
8X-RAY DIFFRACTION8C58 - 109
9X-RAY DIFFRACTION9C110 - 116
10X-RAY DIFFRACTION10D2 - 19
11X-RAY DIFFRACTION11D20 - 94
12X-RAY DIFFRACTION12D95 - 116
13X-RAY DIFFRACTION13E169 - 212
14X-RAY DIFFRACTION14E213 - 229
15X-RAY DIFFRACTION15E230 - 237
16X-RAY DIFFRACTION16F168 - 204
17X-RAY DIFFRACTION17F205 - 229
18X-RAY DIFFRACTION18F230 - 241
19X-RAY DIFFRACTION19G168 - 230
20X-RAY DIFFRACTION20G231 - 236
21X-RAY DIFFRACTION21G237 - 242
22X-RAY DIFFRACTION22H169 - 199
23X-RAY DIFFRACTION23H200 - 233
24X-RAY DIFFRACTION24H234 - 238

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