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- PDB-3fdq: Recognition of AT-rich DNA binding sites by the MogR Repressor -

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Basic information

Entry
Database: PDB / ID: 3fdq
TitleRecognition of AT-rich DNA binding sites by the MogR Repressor
Components
  • 5'-D(*AP*TP*TP*TP*TP*TP*TP*AP*AP*AP*AP*AP*AP*AP*T)-3'
  • 5'-D(*TP*AP*TP*TP*TP*TP*TP*TP*TP*AP*AP*AP*AP*AP*A)-3'
  • Motility gene repressor mogR
KeywordsDNA BINDING PROTEIN/DNA / Protein-DNA complex / Helix-turn-helix / minor groove binding / Cytoplasm / DNA-binding / Repressor / Transcription / Transcription regulation / Virulence / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


: / DNA-binding transcription repressor activity / protein-DNA complex / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
Motility repressor MogR, DNA-binding domain / Motility repressor MogR, DNA-binding domain / MogR, DNA-binding domain superfamily / DNA binding domain of the motility gene repressor (MogR) / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Motility gene repressor MogR / Motility gene repressor MogR
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsShen, A. / Higgins, D.E. / Panne, D.
CitationJournal: Structure / Year: 2009
Title: Recognition of AT-Rich DNA Binding Sites by the MogR Repressor.
Authors: Shen, A. / Higgins, D.E. / Panne, D.
History
DepositionNov 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Motility gene repressor mogR
B: Motility gene repressor mogR
C: 5'-D(*AP*TP*TP*TP*TP*TP*TP*AP*AP*AP*AP*AP*AP*AP*T)-3'
D: 5'-D(*TP*AP*TP*TP*TP*TP*TP*TP*TP*AP*AP*AP*AP*AP*A)-3'


Theoretical massNumber of molelcules
Total (without water)48,8194
Polymers48,8194
Non-polymers00
Water3,963220
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-25 kcal/mol
Surface area18310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.344, 93.597, 60.768
Angle α, β, γ (deg.)90.00, 113.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Motility gene repressor mogR


Mass: 19823.846 Da / Num. of mol.: 2 / Fragment: DNA binding domain: UNP residues 1-162
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: lmo0674, mogR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8Y960, UniProt: P0DJO8*PLUS
#2: DNA chain 5'-D(*AP*TP*TP*TP*TP*TP*TP*AP*AP*AP*AP*AP*AP*AP*T)-3'


Mass: 4590.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: flaA promoter sequence
#3: DNA chain 5'-D(*TP*AP*TP*TP*TP*TP*TP*TP*TP*AP*AP*AP*AP*AP*A)-3'


Mass: 4581.033 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: flaA promoter sequence
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.58 Å3/Da / Density % sol: 52.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM 2-(N-morpholino)ethanesulfonic acid (MES) pH 6.0, 10-15% w/v PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1MES11
2PEG 400011
3MES12
4PEG 400012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 22, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. all: 49987 / Num. obs: 48556 / % possible obs: 97.1 % / Observed criterion σ(I): 2
Reflection shellResolution: 1.74→1.8 Å / % possible all: 64.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXDphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.75→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2322 2422 RANDOM
Rwork0.2169 --
obs0.2169 48556 -
Solvent computationBsol: 39.534 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.384 Å20 Å2-1.028 Å2
2---5.955 Å20 Å2
3----1.429 Å2
Refinement stepCycle: LAST / Resolution: 1.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2280 609 0 220 3109
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005549
X-RAY DIFFRACTIONc_angle_deg1.10116
LS refinement shellResolution: 1.75→1.83 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.328 268 -
Rwork0.296 --
obs-4679 64.8 %

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