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- PDB-4i8t: C.Esp1396I bound to a 19 base pair DNA duplex -

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Basic information

Entry
Database: PDB / ID: 4i8t
TitleC.Esp1396I bound to a 19 base pair DNA duplex
Components
  • DNA (5'-D(P*TP*GP*TP*GP*TP*GP*AP*TP*TP*AP*TP*AP*GP*TP*CP*AP*AP*CP*A)-3')
  • DNA (5'-D(P*TP*GP*TP*TP*GP*AP*CP*TP*AP*TP*AP*AP*TP*CP*AP*CP*AP*CP*A)-3')
  • Regulatory protein
KeywordsTranscription/DNA / Restriction-modification / helix-turn-helix / transcriptional regulator / DNA / Transcription-DNA complex
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / cytosol
Similarity search - Function
: / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Regulatory protein
Similarity search - Component
Biological speciesEnterobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsMartin, R.N.A. / McGeehan, J.E. / Kneale, G.G.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Structural analysis of DNA-protein complexes regulating the restriction-modification system Esp1396I.
Authors: Martin, R.N. / McGeehan, J.E. / Ball, N.J. / Streeter, S.D. / Thresh, S.J. / Kneale, G.G.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structure of the restriction-modification controller protein C.Esp1396I.
Authors: Ball, N. / Streeter, S.D. / Kneale, G.G. / McGeehan, J.E.
#2: Journal: Nucleic Acids Res. / Year: 2012
Title: Recognition of dual symmetry by the controller protein C.Esp1396I based on the structure of the transcriptional activation complex.
Authors: McGeehan, J.E. / Ball, N.J. / Streeter, S.D. / Thresh, S.J. / Kneale, G.G.
#3: Journal: Nucleic Acids Res. / Year: 2012
Title: The structural basis of differential DNA sequence recognition by restriction-modification controller proteins.
Authors: Ball, N.J. / McGeehan, J.E. / Streeter, S.D. / Thresh, S.J. / Kneale, G.G.
#4: Journal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structure of the restriction-modification controller protein C.Esp1396I.
Authors: Ball, N. / Streeter, S.D. / Kneale, G.G. / McGeehan, J.E.
History
DepositionDec 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Regulatory protein
B: Regulatory protein
C: DNA (5'-D(P*TP*GP*TP*TP*GP*AP*CP*TP*AP*TP*AP*AP*TP*CP*AP*CP*AP*CP*A)-3')
D: DNA (5'-D(P*TP*GP*TP*GP*TP*GP*AP*TP*TP*AP*TP*AP*GP*TP*CP*AP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)30,6894
Polymers30,6894
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-31 kcal/mol
Surface area14530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.510, 60.860, 80.350
Angle α, β, γ (deg.)90.00, 113.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Regulatory protein


Mass: 9521.175 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter sp. (bacteria) / Strain: RFL1396 / Gene: esp1396IC / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q8GGH0
#2: DNA chain DNA (5'-D(P*TP*GP*TP*TP*GP*AP*CP*TP*AP*TP*AP*AP*TP*CP*AP*CP*AP*CP*A)-3')


Mass: 5787.785 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesised DNA Oligonucleotide
#3: DNA chain DNA (5'-D(P*TP*GP*TP*GP*TP*GP*AP*TP*TP*AP*TP*AP*GP*TP*CP*AP*AP*CP*A)-3')


Mass: 5858.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesised DNA Oligonucleotide

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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: 2.76 Å3/Da / Density % sol: 55.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M PCTP buffer, 25 % w/v PEG 1500, 10 mM Spermidine, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979493 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 2, 2011
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979493 Å / Relative weight: 1
ReflectionResolution: 3→73.702 Å / Num. all: 22560 / Num. obs: 6809 / % possible obs: 99.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 5.9
Reflection shellResolution: 3→3.21 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.013 / Mean I/σ(I) obs: 0.9 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å45.72 Å
Translation3 Å45.72 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.1.26data scaling
PHASER2.5.1phasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
GDAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3G5G

3g5g


Resolution: 3→44.434 Å / Occupancy max: 1 / Occupancy min: 0.14 / SU ML: 0.34 / σ(F): 1.91 / Phase error: 32.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2934 326 4.79 %
Rwork0.2385 --
obs0.2412 6799 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 104.5102 Å2
Refinement stepCycle: LAST / Resolution: 3→44.434 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1220 779 0 0 1999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032134
X-RAY DIFFRACTIONf_angle_d0.7373030
X-RAY DIFFRACTIONf_dihedral_angle_d22.102885
X-RAY DIFFRACTIONf_chiral_restr0.042356
X-RAY DIFFRACTIONf_plane_restr0.001241

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