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- PDB-1m1f: Kid toxin protein from E.coli plasmid R1 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1m1f
TitleKid toxin protein from E.coli plasmid R1
ComponentsKid toxin protein
KeywordsTOXIN / Toxin-Antitoxin / Plasmid Maintenance / Post segregational killing / DNA replication / Mutational Analysis / CcdB
Function / homology
Function and homology information


endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / RNA binding
Similarity search - Function
SH3 type barrels. - #110 / mRNA interferase PemK-like / PemK-like, MazF-like toxin of type II toxin-antitoxin system / Plasmid maintenance toxin/Cell growth inhibitor / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Endoribonuclease PemK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsHargreaves, D. / Santos-Sierra, S. / Giraldo, R. / Sabariegos-Jareno, R. / de la Cueva-Mendez, G. / Boelens, R. / Diaz-Orejas, R. / Rafferty, J.B.
CitationJournal: Structure / Year: 2002
Title: Structural and Functional Analysis of the Kid toxin protein from E.coli plasmid R1
Authors: Hargreaves, D. / Santos-Sierra, S. / Giraldo, R. / Sabariegos-Jareno, R. / de la Cueva-Mendez, G. / Boelens, R. / Diaz-Orejas, R. / Rafferty, J.B.
History
DepositionJun 19, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_remark / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_remark.text / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999Sequence: The database reference sequence for PemK protein (SwissProt accession number P13976) is ...Sequence: The database reference sequence for PemK protein (SwissProt accession number P13976) is the closest match to Kid toxin protein. Their sequences are identical, however PemK has a long leader sequence not present in Kid toxin protein.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kid toxin protein
B: Kid toxin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8863
Polymers23,7922
Non-polymers951
Water7,800433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-18 kcal/mol
Surface area9100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.264, 45.457, 65.021
Angle α, β, γ (deg.)90.00, 96.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Kid toxin protein


Mass: 11895.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: R1 / Production host: Escherichia coli (E. coli) / References: UniProt: P13976
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 433 / 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: 2.05 Å3/Da / Density % sol: 40.09 %
Crystal growTemperature: 290 K / pH: 5.8
Details: potassium phosphate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K, pH 5.80
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Hargreaves, D., (2002) Acta Crystallogr., D58, 355.
pH: 5.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.4-1.5 M1reservoirNaCl
2100 mMpotassium phosphate1droppH5.8
32-2.5 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97965, 0.97979, 0.96863
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 25, 2001
RadiationMonochromator: CRYSTAL / Protocol: 3 WAVELENGTH MA / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979651
20.979791
30.968631
ReflectionResolution: 1.4→25 Å / Num. obs: 43111 / % possible obs: 93 % / Observed criterion σ(I): 3 / Redundancy: 5.1 % / Rmerge(I) obs: 0.042 / Rsym value: 0.033 / Net I/σ(I): 3
Reflection shellResolution: 1.39→1.43 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 3 / Rsym value: 0.09 / % possible all: 87.8
Reflection
*PLUS
Highest resolution: 1.25 Å / Lowest resolution: 12 Å

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
REFMAC5refinement
CCP4phasing
RefinementMethod to determine structure: MAD / Resolution: 1.4→12 Å / SU B: 2.069 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.056 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.18187 2195 5.1 %random
Rwork0.16013 ---
obs0.16126 40455 79.83 %-
Displacement parametersBiso mean: 9.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å2-0.09 Å2
2---0.06 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.4→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1571 0 5 454 2030
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.022
X-RAY DIFFRACTIONp_angle_d1.3361.97
X-RAY DIFFRACTIONp_planar_d0.0040.02
X-RAY DIFFRACTIONp_hb_or_metal_coord0.2020.3
X-RAY DIFFRACTIONp_plane_restr0.0040.02
X-RAY DIFFRACTIONp_chiral_restr0.0710.2
X-RAY DIFFRACTIONp_singtor_nbd4.2763
X-RAY DIFFRACTIONp_multtor_nbd18.43615
X-RAY DIFFRACTIONp_xyhbond_nbd0.3080.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1110.5
X-RAY DIFFRACTIONp_mcbond_it0.7931.5
X-RAY DIFFRACTIONp_mcangle_it1.3412
X-RAY DIFFRACTIONp_scbond_it1.8053
X-RAY DIFFRACTIONp_scangle_it2.7574.5
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.275 46
Rwork0.212 792
Refinement
*PLUS
Highest resolution: 1.25 Å / Lowest resolution: 12 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.182 / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.022
X-RAY DIFFRACTIONp_planar_d0.0040.02
X-RAY DIFFRACTIONp_plane_restr0.0040.02
X-RAY DIFFRACTIONp_chiral_restr0.0710.2
X-RAY DIFFRACTIONp_mcbond_it0.793
LS refinement shell
*PLUS
Highest resolution: 1.25 Å / Lowest resolution: 1.28 Å / Rfactor Rfree: 0.31 / Rfactor Rwork: 0.24

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