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- PDB-3kxe: A conserved mode of protein recognition and binding in a ParD-Par... -

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Basic information

Entry
Database: PDB / ID: 3kxe
TitleA conserved mode of protein recognition and binding in a ParD-ParE toxin-antitoxin complex
Components
  • Antitoxin protein parD-1
  • Toxin protein parE-1
KeywordsPROTEIN BINDING / toxin / antitoxin / complex / Caulobacter / TA system
Function / homology
Function and homology information


protein heterotetramerization / regulation of DNA-templated transcription / protein homodimerization activity
Similarity search - Function
Antitoxin ParD1-like / Toxin-antitoxin system, toxin component ParE1/4 / Bacterial antitoxin of ParD toxin-antitoxin type II system and RHH / Antitoxin ParD / Antitoxin ParD superfamily / : / ParE toxin of type II toxin-antitoxin system, parDE / RelE-like / Toxin-antitoxin system, RelE/ParE toxin family / Helicase, Ruva Protein; domain 3 ...Antitoxin ParD1-like / Toxin-antitoxin system, toxin component ParE1/4 / Bacterial antitoxin of ParD toxin-antitoxin type II system and RHH / Antitoxin ParD / Antitoxin ParD superfamily / : / ParE toxin of type II toxin-antitoxin system, parDE / RelE-like / Toxin-antitoxin system, RelE/ParE toxin family / Helicase, Ruva Protein; domain 3 / YaeB-like fold / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / Ribbon-helix-helix / Helix non-globular / Special / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Toxin / Antitoxin protein parD1 / Antitoxin ParD1 / Toxin ParE1
Similarity search - Component
Biological speciesCaulobacter crescentus NA1000 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsCrosson, S. / Dalton, K.
CitationJournal: Biochemistry / Year: 2010
Title: A Conserved Mode of Protein Recognition and Binding in a ParD-ParE Toxin-Antitoxin Complex.
Authors: Dalton, K.M. / Crosson, S.
History
DepositionDec 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Toxin protein parE-1
B: Toxin protein parE-1
C: Antitoxin protein parD-1
D: Antitoxin protein parD-1


Theoretical massNumber of molelcules
Total (without water)45,1494
Polymers45,1494
Non-polymers00
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10710 Å2
ΔGint-59 kcal/mol
Surface area16380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.735, 72.707, 76.814
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 Toxin protein parE-1


Mass: 12928.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus NA1000 (bacteria)
Strain: NA1000 / CB15N / Gene: CCNA_00916, parD-1, parE-1 / Plasmid: pET-Duet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B8H242, UniProt: Q9A9T8*PLUS
#2: Protein Antitoxin protein parD-1


Mass: 9645.529 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus NA1000 (bacteria)
Strain: NA1000 / CB15N / Gene: CCNA_00917, parD-1, parE-1 / Plasmid: pET-Duet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B8H243, UniProt: P58091*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.03 Å3/Da / Density % sol: 39.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM MES, 100 mM (NH4)2HPO3, 10% PEG 20,000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-E10.97
SYNCHROTRONAPS 21-ID-D20.97
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Feb 9, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.6→33.96 Å / Num. obs: 11711 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2.5
Reflection shellResolution: 2.6→2.66 Å / % possible all: 98

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.6→33.96 Å / SU ML: 0.38 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2916 557 4.76 %RANDOM
Rwork0.2367 ---
obs0.2393 11141 98.81 %-
all-11840 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.248 Å2 / ksol: 0.321 e/Å3
Refinement stepCycle: LAST / Resolution: 2.6→33.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2685 0 0 46 2731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142731
X-RAY DIFFRACTIONf_angle_d1.543677
X-RAY DIFFRACTIONf_dihedral_angle_d20.1511001
X-RAY DIFFRACTIONf_chiral_restr0.101387
X-RAY DIFFRACTIONf_plane_restr0.006493
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.8570.35751340.2692645X-RAY DIFFRACTION96
2.857-3.27010.33221500.25322766X-RAY DIFFRACTION100
3.2701-4.11890.26881280.21392819X-RAY DIFFRACTION100
4.1189-33.96290.26561450.23472924X-RAY DIFFRACTION99

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