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- PDB-5e20: Crystal structure of the organohalide sensing RdhR-CbdbA1625 tran... -

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Basic information

Entry
Database: PDB / ID: 5.0E+20
TitleCrystal structure of the organohalide sensing RdhR-CbdbA1625 transcriptional regulator in the 2,3-dichlorophenol bound form
ComponentsTranscriptional regulator, MarR family
KeywordsTRANSCRIPTION / MarR transcriptional regulator / organohalide binding / DNA binding
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
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
2,3-dichlorophenol / Transcriptional regulator, MarR family / :
Similarity search - Component
Biological speciesDehalococcoides sp. CBDB1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsQuezada, C.P. / Dunstan, M.S. / Fisher, K. / Leys, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research CouncilDEHALORES206080 United Kingdom
CitationJournal: To be published
Title: Crystal structures of RdhRCbdbA1625 provide insight into sensing of chloroaromatic compounds by MarR-type regulators
Authors: Quezada, C.P. / Dunstan, M.S. / Fisher, K. / Leys, D.
History
DepositionSep 30, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator, MarR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1792
Polymers21,0161
Non-polymers1631
Water1,58588
1
A: Transcriptional regulator, MarR family
hetero molecules

A: Transcriptional regulator, MarR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3594
Polymers42,0332
Non-polymers3262
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area7950 Å2
ΔGint-62 kcal/mol
Surface area17810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.320, 71.320, 87.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-380-

HOH

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Components

#1: Protein Transcriptional regulator, MarR family


Mass: 21016.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dehalococcoides sp. CBDB1 (bacteria) / Gene: rdhR, btf_1489 / Production host: Escherichia coli (E. coli) / References: UniProt: M1R817, UniProt: A0A1I9GEQ5*PLUS
#2: Chemical ChemComp-5JF / 2,3-dichlorophenol


Mass: 163.001 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H4Cl2O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 3.04 Å3/Da / Density % sol: 59.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: Crystals formed in 0.1M Tris pH 7.5, 0.3M sodium acetate, 15% w/v PEG 4K were flash-cooled in liquid nitrogen by supplementing the mother liquor with 10% PEG 200

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.987 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.97→50.39 Å / Num. obs: 17630 / % possible obs: 99.9 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 24.4
Reflection shellResolution: 1.97→2.02 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 3.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
REFMAC5.8.0049phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E1W

5e1w


Resolution: 1.97→50.39 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.324 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23412 950 5.1 %RANDOM
Rwork0.19101 ---
obs0.19315 17630 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.702 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20.36 Å20 Å2
2--0.72 Å20 Å2
3----2.32 Å2
Refinement stepCycle: 1 / Resolution: 1.97→50.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1373 0 9 88 1470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0191494
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0061.9692028
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5525190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.92323.54862
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.03115297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.049159
X-RAY DIFFRACTIONr_chiral_restr0.1450.2235
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021080
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.693.012712
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.5314.495897
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.5163.373782
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.25725.3582280
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.97→2.021 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 70 -
Rwork0.247 1274 -
obs--99.85 %

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