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- PDB-2fkd: Crystal Structure of the C-terminal domain of Bacteriophage 186 r... -

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Basic information

Entry
Database: PDB / ID: 2fkd
TitleCrystal Structure of the C-terminal domain of Bacteriophage 186 repressor
ComponentsRepressor protein CI
KeywordsTranscription regulator / genetic switch / regulation / cooperativity / repressor
Function / homology
Function and homology information


protein complex oligomerization / negative regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Bacteriophage CI repressor, N-terminal / Bacteriophage CI repressor, C-terminal / Bacteriophage CI repressor helix-turn-helix domain / Bacteriophage CI repressor C-terminal domain / Umud Fragment, subunit A / Umud Fragment, subunit A / Lambda repressor-like, DNA-binding domain superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Repressor protein CI
Similarity search - Component
Biological speciesEnterobacteria phage 186 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsLewis, M.
CitationJournal: Mol.Cell / Year: 2006
Title: The structural basis of cooperative regulation at an alternate genetic switch.
Authors: Pinkett, H.W. / Shearwin, K.E. / Stayrook, S. / Dodd, I.B. / Burr, T. / Hochschild, A. / Egan, J.B. / Lewis, M.
History
DepositionJan 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Repressor protein CI
B: Repressor protein CI
C: Repressor protein CI
D: Repressor protein CI
E: Repressor protein CI
F: Repressor protein CI
G: Repressor protein CI
H: Repressor protein CI
I: Repressor protein CI
J: Repressor protein CI
K: Repressor protein CI
L: Repressor protein CI
M: Repressor protein CI
N: Repressor protein CI


Theoretical massNumber of molelcules
Total (without water)169,03314
Polymers169,03314
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28820 Å2
ΔGint-73 kcal/mol
Surface area70130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.606, 167.089, 177.068
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is the 14-mer in the asymmetric unit.

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Components

#1: Protein
Repressor protein CI


Mass: 12073.819 Da / Num. of mol.: 14 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage 186 (virus) / Genus: P2-like viruses / Species: Enterobacteria phage P2 / Gene: CI / Production host: Escherichia coli (E. coli) / References: UniProt: P08707

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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: 2.87 Å3/Da / Density % sol: 57.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.29
Details: 23% PEG 1500, 0.1 M Hepes pH 7.29, 10% sucrose, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 29, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 54011 / Num. obs: 54011 / % possible obs: 0.938 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.7→2.87 Å / % possible all: 0.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.7→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.297 3843 RANDOM
Rwork0.24 --
all0.241 54300 -
obs0.241 53867 -
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11886 0 0 0 11886
LS refinement shellResolution: 2.7→20 Å / Rfactor Rfree error: 0.05
RfactorNum. reflection% reflection
Rfree0.298 3843 -
Rwork0.24 --
obs-53867 99.2 %

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