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- PDB-5hlh: Crystal structure of the overoxidized AbfR bound to DNA -

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Basic information

Entry
Database: PDB / ID: 5hlh
TitleCrystal structure of the overoxidized AbfR bound to DNA
Components
  • DNA (5'-D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP*GP*T)-3')
  • MarR family transcriptional regulator
KeywordsTRANSCRIPTION REGULATOR/DNA / transcription factor / oxidation / TRANSCRIPTION REGULATOR-DNA complex
Function / homology
Function and homology information


response to stress / DNA-binding transcription factor activity
Similarity search - Function
: / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / 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) / : / Transcriptional regulator, MarR family
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLiu, G. / Liu, X. / Gan, J. / Yang, C.-G.
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Structural Insights into the Redox-Sensing Mechanism of MarR-Type Regulator AbfR.
Authors: Liu, G. / Liu, X. / Xu, H. / Liu, X. / Zhou, H. / Huang, Z. / Gan, J. / Chen, H. / Lan, L. / Yang, C.G.
History
DepositionJan 15, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Nov 8, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: DNA (5'-D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP*GP*T)-3')
J: DNA (5'-D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP*GP*T)-3')
K: DNA (5'-D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP*GP*T)-3')
L: DNA (5'-D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP*GP*T)-3')
M: DNA (5'-D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP*GP*T)-3')
N: DNA (5'-D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP*GP*T)-3')
O: DNA (5'-D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP*GP*T)-3')
P: DNA (5'-D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP*GP*T)-3')
A: MarR family transcriptional regulator
B: MarR family transcriptional regulator
C: MarR family transcriptional regulator
D: MarR family transcriptional regulator
E: MarR family transcriptional regulator
F: MarR family transcriptional regulator
G: MarR family transcriptional regulator
H: MarR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)198,61916
Polymers198,61916
Non-polymers00
Water00
1
I: DNA (5'-D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP*GP*T)-3')
J: DNA (5'-D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP*GP*T)-3')
A: MarR family transcriptional regulator
B: MarR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)49,6554
Polymers49,6554
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11830 Å2
ΔGint-80 kcal/mol
Surface area20510 Å2
MethodPISA
2
K: DNA (5'-D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP*GP*T)-3')
L: DNA (5'-D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP*GP*T)-3')
C: MarR family transcriptional regulator
D: MarR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)49,6554
Polymers49,6554
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11700 Å2
ΔGint-83 kcal/mol
Surface area20120 Å2
MethodPISA
3
M: DNA (5'-D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP*GP*T)-3')
N: DNA (5'-D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP*GP*T)-3')
E: MarR family transcriptional regulator
F: MarR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)49,6554
Polymers49,6554
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11900 Å2
ΔGint-81 kcal/mol
Surface area20470 Å2
MethodPISA
4
O: DNA (5'-D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP*GP*T)-3')
P: DNA (5'-D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP*GP*T)-3')
G: MarR family transcriptional regulator
H: MarR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)49,6554
Polymers49,6554
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11810 Å2
ΔGint-84 kcal/mol
Surface area19880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.305, 290.914, 52.351
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: DNA chain
DNA (5'-D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP*GP*T)-3')


Mass: 7369.767 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein
MarR family transcriptional regulator


Mass: 17457.662 Da / Num. of mol.: 8 / Mutation: L72M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis (bacteria) / Gene: ADT70_02765 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0N1EJ89, UniProt: Q5HKZ1*PLUS

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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: 2.88 Å3/Da / Density % sol: 57.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium cacodylate, 100 mM NaCl, 50 mM Mg2Cl, 12% PEG 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9735 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9735 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 43913 / % possible obs: 94.2 % / Redundancy: 4.9 % / Net I/σ(I): 23.3
Reflection shellResolution: 3→3.05 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HBL

4hbl


Resolution: 3→30 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.868 / SU B: 21.084 / SU ML: 0.373 / Cross valid method: THROUGHOUT / ESU R Free: 0.471 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27235 2236 5 %RANDOM
Rwork0.22393 ---
obs0.22648 42122 93.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 75.168 Å2
Baniso -1Baniso -2Baniso -3
1-6.8 Å20 Å2-0 Å2
2---6.85 Å2-0 Å2
3---0.05 Å2
Refinement stepCycle: 1 / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9037 3912 0 0 12949
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01713564
X-RAY DIFFRACTIONr_bond_other_d0.0030.0211002
X-RAY DIFFRACTIONr_angle_refined_deg1.491.68319106
X-RAY DIFFRACTIONr_angle_other_deg1.169325428
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.47651068
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.13625.133487
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.642151783
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5951556
X-RAY DIFFRACTIONr_chiral_restr0.0790.21955
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212572
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023164
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.667.7214320
X-RAY DIFFRACTIONr_mcbond_other4.6597.7214319
X-RAY DIFFRACTIONr_mcangle_it7.05911.5695372
X-RAY DIFFRACTIONr_mcangle_other7.05911.5695373
X-RAY DIFFRACTIONr_scbond_it4.7397.3619244
X-RAY DIFFRACTIONr_scbond_other4.7387.369242
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.25410.87613734
X-RAY DIFFRACTIONr_long_range_B_refined9.52360.66516052
X-RAY DIFFRACTIONr_long_range_B_other9.52460.66716053
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 170 -
Rwork0.337 3257 -
obs--99.45 %

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