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- PDB-4ntq: CdiA-CT/CdiI toxin and immunity complex from Enterobacter cloacae -

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Basic information

Entry
Database: PDB / ID: 4ntq
TitleCdiA-CT/CdiI toxin and immunity complex from Enterobacter cloacae
Components
  • Contact-dependent inhibitor A
  • ECL CdiI
KeywordsTOXIN / RNase / immunity
Function / homology
Function and homology information


RNA endonuclease activity / toxin activity / Hydrolases; Acting on ester bonds / host cell cytoplasm
Similarity search - Function
Novel toxin 21 (CdiA), C-terminal domain / Secreted effector protein pipB2 fold - #20 / Novel toxin 21 / Novel toxin 21 superfamily / CdiI, C-terminal / : / Novel toxin 21 / CdiI N-terminal domain / Secreted effector protein pipB2 fold / Ribonuclease domain of colicin e3 (Residues 456-551) ...Novel toxin 21 (CdiA), C-terminal domain / Secreted effector protein pipB2 fold - #20 / Novel toxin 21 / Novel toxin 21 superfamily / CdiI, C-terminal / : / Novel toxin 21 / CdiI N-terminal domain / Secreted effector protein pipB2 fold / Ribonuclease domain of colicin e3 (Residues 456-551) / 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 / Pectin lyase fold / Pectin lyase fold/virulence factor / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Immunity protein CdiI / 16S rRNA endonuclease CdiA
Similarity search - Component
Biological speciesEnterobacter cloacae subsp. cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMorse, R.P. / Goulding, C.W.
CitationJournal: Structure / Year: 2014
Title: CdiA from Enterobacter cloacae Delivers a Toxic Ribosomal RNase into Target Bacteria.
Authors: Beck, C.M. / Morse, R.P. / Cunningham, D.A. / Iniguez, A. / Low, D.A. / Goulding, C.W. / Hayes, C.S.
History
DepositionDec 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Contact-dependent inhibitor A
B: ECL CdiI


Theoretical massNumber of molelcules
Total (without water)43,3472
Polymers43,3472
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-8 kcal/mol
Surface area10460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.250, 85.250, 74.913
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Contact-dependent inhibitor A


Mass: 25046.920 Da / Num. of mol.: 1 / Fragment: UNP residues 3087-3321
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae subsp. cloacae (bacteria)
Strain: ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56 / Gene: cdiA, ECL_04451 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D5CBA0
#2: Protein ECL CdiI


Mass: 18299.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae subsp. cloacae (bacteria)
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A023GPJ0*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsCHAIN A RESIDUES 1-159 WERE PART OF THE PURIFIED PROTEIN SAMPLE, BUT THE PROTEIN UNDERWENT ...CHAIN A RESIDUES 1-159 WERE PART OF THE PURIFIED PROTEIN SAMPLE, BUT THE PROTEIN UNDERWENT DEGRADATION DURING THE LENGTHY CRYSTALLIZATION PROCESS AND THOSE RESIDUES ARE NOT IN THE FINAL STRUCTURE.

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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: 1.57 Å3/Da / Density % sol: 21.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: 1.5 M ammonium sulfate, 0.1 M Bis Tris pH 5.1, 1% PEG-3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 3, 2012
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 11315 / % possible obs: 100 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 29.3 % / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXAutoMRmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXAutoMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→38.125 Å / SU ML: 0.25 / σ(F): 1.38 / Phase error: 23.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2373 538 4.76 %Random
Rwork0.1833 ---
obs0.1859 11291 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→38.125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1750 0 0 62 1812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081807
X-RAY DIFFRACTIONf_angle_d1.1532450
X-RAY DIFFRACTIONf_dihedral_angle_d14.278647
X-RAY DIFFRACTIONf_chiral_restr0.078255
X-RAY DIFFRACTIONf_plane_restr0.004321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3996-2.64110.3161270.21062613X-RAY DIFFRACTION99
2.6411-3.02310.28791290.2242649X-RAY DIFFRACTION100
3.0231-3.80820.24621430.18542660X-RAY DIFFRACTION100
3.8082-38.12980.19591390.16272831X-RAY DIFFRACTION100
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)
15.4622-1.79072.43613.5681-1.76144.9110.38660.67182.19050.2545-0.35780.0403-0.91530.90330.10360.8489-0.2320.34170.0628-0.03381.0388-24.419328.729-6.8241
29.9843-7.67344.7617.9629-7.69571.9960.37431.8123-2.8695-2.4482-0.01491.66011.1936-0.8509-0.71160.9425-0.17170.11390.4981-0.09211.064-31.36818.8776-18.786
34.63340.2648-0.11063.55810.44762.19410.15620.06410.7580.48110.20730.5906-0.6308-0.3322-0.47310.46310.06180.22320.26410.06850.502-35.210619.1346-7.1378
47.26825.0836-3.01024.978-3.89083.45070.32750.17360.74260.3586-0.0620.475-0.45870.3367-0.17360.2916-0.01930.04270.3144-0.0480.2386-18.514811.497-17.4552
55.86631.6849-0.21712.9099-0.89255.3594-0.20650.7392-0.1848-0.20190.1978-0.0098-0.44160.36370.0410.2774-0.01840.03310.3018-0.03060.1698-19.718511.1651-13.1185
69.38936.114-5.89346.1072-6.10215.88220.2046-1.0125-0.62881.0666-0.7931-0.6985-1.08841.30880.51120.2983-0.0599-0.01380.3506-0.0170.2614-14.34442.11-4.4323
74.7211-1.2623-0.41190.65871.25254.18710.086-0.8919-0.06370.4495-0.01240.4489-0.16650.3029-0.01930.281-0.03280.03750.4058-0.03940.1528-22.56681.04560.9272
80.76260.60651.14692.43652.24222.68080.3676-0.65480.73570.57960.0278-0.3577-0.91591.3024-0.36060.5753-0.2580.07190.6477-0.13050.3992-12.903718.4618-3.0073
94.8883-2.5427-0.4411.31540.24014.24710.0711-0.2884-0.01580.73470.03220.564-0.02020.2423-0.06590.3685-0.07870.08440.2291-0.01960.2103-26.81636.6393-2.1162
100.43370.10860.1640.038-0.0440.79270.1292-1.08990.3620.87590.4514-0.33150.4896-0.4140.81810.7329-0.364-0.10161.5398-0.06760.4697-14.708818.99515.8882
116.1174.97590.59912.0033-3.74342.65341.5005-1.63160.76281.7075-0.47350.5541-1.13041.9803-0.26640.8996-0.3891-0.01680.8311-0.04440.3242-15.47898.63194.6342
124.6868-3.6624-1.07034.3070.20821.5812-0.0579-0.50260.30370.53320.18820.5295-0.3335-0.4736-0.17110.5793-0.03430.24180.3192-0.03470.4767-35.48811.11332.3465
136.364-3.4782-2.23946.9381-0.27493.4393-0.38560.193-0.65420.6011-0.17580.40720.5107-0.07170.52180.4461-0.05350.08420.2193-0.04890.2024-23.0514-4.0447-8.6144
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 162 through 203 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 204 through 213 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 214 through 235 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 25 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 26 through 40 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 41 through 58 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 59 through 65 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 66 through 75 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 76 through 97 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 98 through 105 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 106 through 112 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 113 through 128 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 129 through 144 )B0

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