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- PDB-5e01: Crystal structure of HiNmlR, a MerR family regulator lacking the ... -

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Basic information

Entry
Database: PDB / ID: 50
TitleCrystal structure of HiNmlR, a MerR family regulator lacking the sensor domain, bound to palyndromic promoter DNA
Components
  • 5'-D(*CP*TP*TP*AP*GP*AP*GP*TP*GP*CP*AP*CP*TP*CP*TP*AP*AP*G)-3'
  • Uncharacterized HTH-type transcriptional regulator HI_0186
KeywordsTRANSCRIPTION / Transcription factor / MerR / thiol-based genetic switch / DNA untwisting
Function / homology
Function and homology information


DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
MerR family regulatory protein / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 - #10 / MerR-type HTH domain signature. / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / : / MerR HTH family regulatory protein / helix_turn_helix, mercury resistance / MerR-type HTH domain profile. / MerR-type HTH domain / Putative DNA-binding domain superfamily ...MerR family regulatory protein / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 - #10 / MerR-type HTH domain signature. / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / : / MerR HTH family regulatory protein / helix_turn_helix, mercury resistance / MerR-type HTH domain profile. / MerR-type HTH domain / Putative DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Uncharacterized HTH-type transcriptional regulator HI_0186
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
Haemophilus influenzae Rd KW20 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCounago, R.M. / Chang, C.W. / Chen, N.H. / Djoko, K.Y. / McEwan, A.G. / Kobe, B.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Structural basis of thiol-based regulation of formaldehyde detoxification in H. influenzae by a MerR regulator with no sensor region.
Authors: Counago, R.M. / Chen, N.H. / Chang, C.W. / Djoko, K.Y. / McEwan, A.G. / Kobe, B.
History
DepositionSep 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized HTH-type transcriptional regulator HI_0186
B: Uncharacterized HTH-type transcriptional regulator HI_0186
C: 5'-D(*CP*TP*TP*AP*GP*AP*GP*TP*GP*CP*AP*CP*TP*CP*TP*AP*AP*G)-3'
D: 5'-D(*CP*TP*TP*AP*GP*AP*GP*TP*GP*CP*AP*CP*TP*CP*TP*AP*AP*G)-3'


Theoretical massNumber of molelcules
Total (without water)40,4454
Polymers40,4454
Non-polymers00
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7630 Å2
ΔGint-64 kcal/mol
Surface area18920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.160, 112.640, 103.790
Angle α, β, γ (deg.)90.00, 101.84, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Uncharacterized HTH-type transcriptional regulator HI_0186


Mass: 14706.960 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (bacteria)
Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: HI_0186 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21De(3) / References: UniProt: P44558
#2: DNA chain 5'-D(*CP*TP*TP*AP*GP*AP*GP*TP*GP*CP*AP*CP*TP*CP*TP*AP*AP*G)-3'


Mass: 5515.591 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Modified promoter element for adhC/NmlR genes from Haemophilus influenzae.
Source: (synth.) Haemophilus influenzae Rd KW20 (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 3.97 Å3/Da / Density % sol: 69.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20 % w/v PEG 3,350; 0.4 M sodium nitrate; 0.1 M Bis-Tris propane pH 7.5; 2 mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Mar 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→19.86 Å / Num. obs: 27932 / Biso Wilson estimate: 66.61 Å2
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 3.8 % / Rmerge(I) obs: 3.264 / % possible all: 77.2

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GPV

3gpv


Resolution: 2.3→19.86 Å / Cor.coef. Fo:Fc: 0.9414 / Cor.coef. Fo:Fc free: 0.931 / SU R Cruickshank DPI: 0.217 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.227 / SU Rfree Blow DPI: 0.186 / SU Rfree Cruickshank DPI: 0.182
RfactorNum. reflection% reflectionSelection details
Rfree0.2435 1424 5.1 %RANDOM
Rwork0.219 ---
obs0.2202 27932 99.58 %-
Displacement parametersBiso mean: 68.16 Å2
Baniso -1Baniso -2Baniso -3
1-1.3862 Å20 Å2-5.8652 Å2
2---1.8937 Å20 Å2
3---0.5075 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2041 732 0 228 3001
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112889HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.024037HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1188SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes54HARMONIC2
X-RAY DIFFRACTIONt_gen_planes327HARMONIC5
X-RAY DIFFRACTIONt_it2889HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.04
X-RAY DIFFRACTIONt_other_torsion3.51
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion379SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3238SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.39 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2797 133 4.55 %
Rwork0.2427 2790 -
all0.2444 2923 -
obs--99.83 %

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