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- PDB-6lxl: Crystal structure of C-terminal DNA-binding domain of Escherichia... -

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Basic information

Entry
Database: PDB / ID: 6lxl
TitleCrystal structure of C-terminal DNA-binding domain of Escherichia coli OmpR
ComponentsTranscriptional regulatory protein OmpR
KeywordsDNA BINDING PROTEIN / DNA binding protein Transcription factor / TRANSCRIPTION
Function / homology
Function and homology information


phosphorelay response regulator activity / phosphorelay signal transduction system / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / cytosol
Similarity search - Function
OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA-binding dual transcriptional regulator OmpR / DNA-binding dual transcriptional regulator OmpR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.56 Å
AuthorsSadotra, S. / Chen, C. / Hsu, C.H.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)108-2628-B-002-013 Taiwan
Ministry of Science and Technology (MoST, Taiwan)108-2113-M-002-011 Taiwan
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Structural basis for promoter DNA recognition by the response regulator OmpR.
Authors: Sadotra, S. / Lou, Y.C. / Tang, H.C. / Chiu, Y.C. / Hsu, C.H. / Chen, C.
History
DepositionFeb 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulatory protein OmpR


Theoretical massNumber of molelcules
Total (without water)13,0991
Polymers13,0991
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, monomeric protein
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.297, 60.297, 83.748
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Transcriptional regulatory protein OmpR


Mass: 13099.091 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ompR, NCTC10764_03768 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A376JR14, UniProt: P0AA16*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: 2.99 Å3/Da / Density % sol: 58.9 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / Details: 0.1 M CHES pH 9.5 10% PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.975 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 3.56→29.88 Å / Num. obs: 2548 / % possible obs: 100 % / Redundancy: 8.4 % / Biso Wilson estimate: 37.5 Å2 / CC1/2: 0.965 / CC star: 0.991 / Rmerge(I) obs: 0.175 / Net I/σ(I): 12.2
Reflection shellResolution: 3.56→3.69 Å / Num. unique obs: 2039 / CC1/2: 0.891

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NHJ

4nhj


Resolution: 3.56→29.88 Å / SU ML: 0.4656 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.235 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3187 247 9.69 %
Rwork0.234 2301 -
obs0.2422 2548 72.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.92 Å2
Refinement stepCycle: LAST / Resolution: 3.56→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms724 0 0 0 724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029740
X-RAY DIFFRACTIONf_angle_d0.5421999
X-RAY DIFFRACTIONf_chiral_restr0.0403110
X-RAY DIFFRACTIONf_plane_restr0.0031129
X-RAY DIFFRACTIONf_dihedral_angle_d2.1594454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.56-4.480.3196980.2298877X-RAY DIFFRACTION55.46
4.48-29.880.31811490.23651424X-RAY DIFFRACTION89.22

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