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- PDB-2f1n: Structure of CdtB, the biologically active subunit of Cytolethal ... -

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Basic information

Entry
Database: PDB / ID: 2f1n
TitleStructure of CdtB, the biologically active subunit of Cytolethal Distending Toxin
ComponentsCytolethal distending toxin subunit B
KeywordsTOXIN / cytolethal distending toxin / CDT / e.coli / DNase I / microbatch
Function / homology
Function and homology information


toxin activity / endonuclease activity / Hydrolases; Acting on ester bonds / extracellular region
Similarity search - Function
Cytolethal distending toxin B / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Cytolethal distending toxin subunit B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsHontz, J.S. / Yoder, M.D. / Dreyfus, L.A.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Differences in Crystal and Solution Structures of the Cytolethal Distending Toxin B Subunit: RELEVANCE TO NUCLEAR TRANSLOCATION AND FUNCTIONAL ACTIVATION.
Authors: Hontz, J.S. / Villar-Lecumberri, M.T. / Potter, B.M. / Yoder, M.D. / Dreyfus, L.A. / Laity, J.H.
History
DepositionNov 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 999SEQUENCE THE cdtABC OPERON WAS CLONED FROM AN E. COLI 9142-88 CHROMOSOMAL DNA GENE LIBRARY. ...SEQUENCE THE cdtABC OPERON WAS CLONED FROM AN E. COLI 9142-88 CHROMOSOMAL DNA GENE LIBRARY. SEQUENCING OF THE OPERON IDENTIFIED A 2-BASE VARIATION IN cdtB AS COMPARED TO THE PUBLISHED SEQUENCE WHICH RESULTS IN A CHANGE IN TWO CdtB AMINO ACIDS, T57R AND L58V. THE AUTHORS BELIEVE THE VARIATION IN CdtB REPRESENTS A DNA SEQUENCING ERROR IN THE PUBLISHED E. COLI 9142-88 CDT SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytolethal distending toxin subunit B


Theoretical massNumber of molelcules
Total (without water)28,7681
Polymers28,7681
Non-polymers00
Water2,774154
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.884, 47.539, 114.888
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cytolethal distending toxin subunit B / CDT B


Mass: 28768.295 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cdtB / Plasmid: pET-45b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 Star / References: UniProt: Q46669
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 1.89 Å3/Da / Density % sol: 34.99 %
Crystal growTemperature: 295 K / pH: 4
Details: Batch under oil, paraffin oil, 0.1 M ammonium thiocyanate, 0.1 M sodium citrate, 40% (w/v) PEG 8000, pH 4.0, microbatch, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 1, 2005
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→57.74 Å / Num. obs: 23141 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 16.8
Reflection shellResolution: 1.73→1.79 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 4.7 / % possible all: 91.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.701data extraction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1sr4

1sr4


Resolution: 1.73→57.74 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.286 / SU ML: 0.075 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2264 1186 5.1 %RANDOM
Rwork0.19188 ---
obs0.19361 21900 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.889 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å20 Å20 Å2
2--2.02 Å20 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.73→57.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1943 0 0 154 2097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211984
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6461.9342709
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1755252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1310.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021554
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2390.2829
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2430.2131
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.282
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2350.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2761.51263
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.33422042
X-RAY DIFFRACTIONr_scbond_it3.33721
X-RAY DIFFRACTIONr_scangle_it5.434.5667
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.73→1.78 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.311 71
Rwork0.243 1387

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