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- PDB-5d4s: Crystal Structure of AraR(DBD) in complex with operator ORX1 -

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Basic information

Entry
Database: PDB / ID: 5d4s
TitleCrystal Structure of AraR(DBD) in complex with operator ORX1
Components
  • Arabinose metabolism transcriptional repressor
  • DNA (5'-D(*AP*AP*AP*TP*AP*CP*AP*TP*AP*CP*GP*TP*AP*CP*AP*AP*AP*TP*AP*TP*T)-3')
  • DNA (5'-D(*TP*AP*AP*TP*AP*TP*TP*TP*GP*TP*AP*CP*GP*TP*AP*TP*GP*TP*AP*TP*T)-3')
KeywordsTRANSCRIPTION/DNA / AraR / Transcription factor / winged-helix-turn-helix / 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
DNA / DNA (> 10) / Arabinose metabolism transcriptional repressor
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.972 Å
AuthorsJain, D. / Narayanan, N. / Nair, D.T.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Plasticity in Repressor-DNA Interactions Neutralizes Loss of Symmetry in Bipartite Operators.
Authors: Jain, D. / Narayanan, N. / Nair, D.T.
History
DepositionAug 8, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references / Derived calculations
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_assembly_prop.biol_id / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,7424
Polymers32,7424
Non-polymers00
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-25 kcal/mol
Surface area14390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.228, 42.454, 67.211
Angle α, β, γ (deg.)90.00, 114.99, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Arabinose metabolism transcriptional repressor


Mass: 9931.353 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-68
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: araR, araC, yvbS, BSU33970 / Plasmid: pDJN1 / Production host: Escherichia coli (E. coli) / References: UniProt: P96711
#2: DNA chain DNA (5'-D(*TP*AP*AP*TP*AP*TP*TP*TP*GP*TP*AP*CP*GP*TP*AP*TP*GP*TP*AP*TP*T)-3')


Mass: 6457.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*AP*AP*TP*AP*CP*AP*TP*AP*CP*GP*TP*AP*CP*AP*AP*AP*TP*AP*TP*T)-3')


Mass: 6422.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: sodium acetate, PEG 8000, potassium chloride

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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: Mar 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→36 Å / Num. obs: 25149 / % possible obs: 99.8 % / Redundancy: 3.7 % / Net I/σ(I): 10.6

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
SCALEPACKdata scaling
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H0E

4h0e


Resolution: 1.972→35.868 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2414 1249 4.97 %
Rwork0.1949 --
obs0.1972 25121 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.972→35.868 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1204 855 0 161 2220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092185
X-RAY DIFFRACTIONf_angle_d1.2333129
X-RAY DIFFRACTIONf_dihedral_angle_d24.11871
X-RAY DIFFRACTIONf_chiral_restr0.049348
X-RAY DIFFRACTIONf_plane_restr0.007256
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9721-2.0510.29091290.26152611X-RAY DIFFRACTION98
2.051-2.14440.25621300.22372636X-RAY DIFFRACTION99
2.1444-2.25740.27741480.21522632X-RAY DIFFRACTION100
2.2574-2.39880.26961170.21092660X-RAY DIFFRACTION100
2.3988-2.5840.27471400.20962639X-RAY DIFFRACTION100
2.584-2.84390.27031410.21662667X-RAY DIFFRACTION100
2.8439-3.25520.28631380.22172630X-RAY DIFFRACTION99
3.2552-4.10030.2251340.172656X-RAY DIFFRACTION99
4.1003-35.87380.19881720.17062741X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.4129-0.2082-0.47333.49830.42282.54590.0695-0.1066-0.21610.0753-0.2120.30060.3618-0.23420.1420.2318-0.0581-0.01060.1716-0.01950.23388.15427.411610.9911
23.3513-0.24960.68593.24830.32574.08090.13530.21330.44960.0106-0.15280.2931-0.4177-0.14810.0370.22040.0520.03790.16320.02260.268214.17131.03590.515
31.7582-0.1143-1.93691.6419-0.21354.60340.1281-0.24170.2188-0.10960.1122-0.13210.20970.667-0.24030.19580.0115-0.03350.3121-0.03820.270923.08618.50135.3285
41.5659-1.0961-1.17341.57210.78433.7950.1103-0.31860.27270.05540.236-0.130.0890.5718-0.2610.1935-0.0537-0.00130.256-0.0610.240521.45218.55398.2078
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2Chain B
3X-RAY DIFFRACTION3Chain T
4X-RAY DIFFRACTION4Chain U

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