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- PDB-5d90: Crystal structure of HiNmlR, a MerR family regulator lacking the ... -

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Basic information

Entry
Database: PDB / ID: 5d90
TitleCrystal structure of HiNmlR, a MerR family regulator lacking the sensor domain, bound to promoter DNA
ComponentsMerR family regulator protein
KeywordsTRANSCRIPTION / MerR family regulator
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
Uncharacterized HTH-type transcriptional regulator HI_0186
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsCounago, R.M. / Chang, C.W. / 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
DepositionAug 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / 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
B: MerR family regulator protein
D: MerR family regulator protein
A: MerR family regulator protein
C: MerR family regulator protein


Theoretical massNumber of molelcules
Total (without water)62,6114
Polymers62,6114
Non-polymers00
Water2,864159
1
B: MerR family regulator protein
D: MerR family regulator protein


Theoretical massNumber of molelcules
Total (without water)31,3052
Polymers31,3052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-38 kcal/mol
Surface area15260 Å2
MethodPISA
2
A: MerR family regulator protein
C: MerR family regulator protein


Theoretical massNumber of molelcules
Total (without water)31,3052
Polymers31,3052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-41 kcal/mol
Surface area15150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.633, 38.967, 145.549
Angle α, β, γ (deg.)90.00, 97.16, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein
MerR family regulator protein / Apo_NmlR


Mass: 15652.698 Da / Num. of mol.: 4
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 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P44558
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M Bis-Tris pH 6.5, 25 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.972 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.3→19.8 Å / Num. obs: 27154 / % possible obs: 99.8 % / Redundancy: 3.7 % / Net I/σ(I): 6.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Cootmodel building
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→19.8 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2697 1998 7.37 %
Rwork0.2211 --
obs0.2247 27119 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4108 0 0 159 4267
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054158
X-RAY DIFFRACTIONf_angle_d0.8945578
X-RAY DIFFRACTIONf_dihedral_angle_d13.681596
X-RAY DIFFRACTIONf_chiral_restr0.038627
X-RAY DIFFRACTIONf_plane_restr0.004699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.35750.35551390.27361755X-RAY DIFFRACTION100
2.3575-2.42110.34621420.2771783X-RAY DIFFRACTION100
2.4211-2.49220.29521410.271769X-RAY DIFFRACTION100
2.4922-2.57250.31431420.27041783X-RAY DIFFRACTION100
2.5725-2.66420.35981400.26091759X-RAY DIFFRACTION100
2.6642-2.77060.28561420.24641801X-RAY DIFFRACTION100
2.7706-2.89630.29721420.24591767X-RAY DIFFRACTION100
2.8963-3.04850.32041420.23891793X-RAY DIFFRACTION100
3.0485-3.23880.26091430.25481804X-RAY DIFFRACTION100
3.2388-3.48760.28121430.22911794X-RAY DIFFRACTION100
3.4876-3.83630.25161430.19841793X-RAY DIFFRACTION100
3.8363-4.38610.22621430.18591802X-RAY DIFFRACTION100
4.3861-5.50630.22861460.17761835X-RAY DIFFRACTION100
5.5063-19.80240.21121500.17521883X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 4.5858 Å / Origin y: -0.9081 Å / Origin z: -35.8588 Å
111213212223313233
T0.2263 Å20.0033 Å2-0.0028 Å2-0.1771 Å20.0098 Å2--0.219 Å2
L0.2325 °20.0422 °20.094 °2--0.027 °20.0177 °2--0.3206 °2
S0.0063 Å °0.0464 Å °-0.0297 Å °-0.0392 Å °0.0217 Å °0.0431 Å °-0.036 Å °-0.0405 Å °-0.0317 Å °
Refinement TLS groupSelection details: all

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