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- PDB-4egz: Crystal Structure of AraR(DBD) in complex with operator ORR3 -

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Basic information

Entry
Database: PDB / ID: 4egz
TitleCrystal Structure of AraR(DBD) in complex with operator ORR3
Components
  • 5'-D(*AP*AP*AP*TP*TP*TP*GP*TP*CP*CP*GP*TP*AP*TP*AP*CP*AP*TP*TP*TP*T)-3'
  • 5'-D(*TP*AP*AP*AP*AP*TP*GP*TP*AP*TP*AP*CP*GP*GP*AP*CP*AP*AP*AP*TP*T)-3'
  • Arabinose metabolism transcriptional repressor
KeywordsTRANSCRIPTION/DNA / Winged-Helix-turn-helix / transcription factor / DNA binding / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / cytoplasm
Similarity search - Function
Arabinose metabolism transcriptional repressor, ligand-binding domain / Transcriptional regulator LacI/GalR-like, sensor domain / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / Periplasmic binding protein-like domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Periplasmic binding protein-like I / Arc Repressor Mutant, subunit A ...Arabinose metabolism transcriptional repressor, ligand-binding domain / Transcriptional regulator LacI/GalR-like, sensor domain / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / Periplasmic binding protein-like domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Periplasmic binding protein-like I / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / DNA / DNA (> 10) / Arabinose metabolism transcriptional repressor
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsJain, D. / Nair, D.T.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Spacing between core recognition motifs determines relative orientation of AraR monomers on bipartite operators.
Authors: Jain, D. / Nair, D.T.
History
DepositionApr 2, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arabinose metabolism transcriptional repressor
B: Arabinose metabolism transcriptional repressor
T: 5'-D(*AP*AP*AP*TP*TP*TP*GP*TP*CP*CP*GP*TP*AP*TP*AP*CP*AP*TP*TP*TP*T)-3'
U: 5'-D(*TP*AP*AP*AP*AP*TP*GP*TP*AP*TP*AP*CP*GP*GP*AP*CP*AP*AP*AP*TP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0389
Polymers32,7434
Non-polymers2955
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-36 kcal/mol
Surface area14820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.160, 46.160, 171.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Arabinose metabolism transcriptional repressor


Mass: 9931.353 Da / Num. of mol.: 2 / Fragment: N-terminus domain, UNP RESIDUES 1-68
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: araC, araR, BSU33970, yvbS / Plasmid: pDJN1 / Production host: Escherichia coli (E. coli) / Strain (production host): C41DE3 / References: UniProt: P96711
#2: DNA chain 5'-D(*AP*AP*AP*TP*TP*TP*GP*TP*CP*CP*GP*TP*AP*TP*AP*CP*AP*TP*TP*TP*T)-3'


Mass: 6402.168 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*TP*AP*AP*AP*AP*TP*GP*TP*AP*TP*AP*CP*GP*GP*AP*CP*AP*AP*AP*TP*T)-3'


Mass: 6478.249 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.79 Å3/Da / Density % sol: 55.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.1M sodium acetate, 200mM KCl, 25% PEG 8000, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 1, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7_650refinement
RefinementMethod to determine structure: SAD / Resolution: 2.3→40.629 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.928 / SU ML: 0.35 / σ(F): 0 / Phase error: 29.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2712 757 4.98 %
Rwork0.2198 --
obs0.2224 15195 95.92 %
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.56 Å2 / ksol: 0.353 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.827 Å20 Å2-0 Å2
2--6.827 Å20 Å2
3----13.654 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40.629 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1281 855 20 145 2301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012370
X-RAY DIFFRACTIONf_angle_d1.2083254
X-RAY DIFFRACTIONf_dihedral_angle_d24.838900
X-RAY DIFFRACTIONf_chiral_restr0.069359
X-RAY DIFFRACTIONf_plane_restr0.004277
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.47770.41551430.32542692X-RAY DIFFRACTION90
2.4777-2.7270.37491420.28612906X-RAY DIFFRACTION96
2.727-3.12150.29851600.25722964X-RAY DIFFRACTION98
3.1215-3.93220.2661690.19912949X-RAY DIFFRACTION99
3.9322-40.63540.23121430.19782927X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: -20.5273 Å / Origin y: -2.6075 Å / Origin z: -20.3348 Å
111213212223313233
T0.321 Å2-0.0368 Å2-0.0435 Å2-0.3216 Å2-0.0425 Å2--0.2936 Å2
L1.084 °20.1408 °21.0832 °2-0.87 °20.9999 °2--2.1138 °2
S-0.0895 Å °-0.0836 Å °-0.0597 Å °-0.1636 Å °-0.0803 Å °-0.0556 Å °-0.2661 Å °-0.2521 Å °-0.0011 Å °
Refinement TLS groupSelection details: ALL

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