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- PDB-6ont: Structure of the Francisella response regulator 1452 receiver domain -

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Basic information

Entry
Database: PDB / ID: 6ont
TitleStructure of the Francisella response regulator 1452 receiver domain
ComponentsTwo-component response regulator 1452 receiver
KeywordsTRANSCRIPTION / response regulator / transcription regulator
Function / homology
Function and homology information


phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily ...OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Winged helix-like DNA-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Two-component response regulator
Similarity search - Component
Biological speciesFrancisella tularensis subsp. novicida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.803 Å
AuthorsMilton, M.E. / Cavanagh, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01 GM055769 United States
Other private United States
CitationJournal: Front Cell Infect Microbiol / Year: 2020
Title: Francisella novicidaTwo-Component System Response Regulator BfpR Modulates iglC Gene Expression, Antimicrobial Peptide Resistance, and Biofilm Production.
Authors: Dean, S.N. / Milton, M.E. / Cavanagh, J. / van Hoek, M.L.
History
DepositionApr 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Two-component response regulator 1452 receiver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0615
Polymers14,9391
Non-polymers1224
Water1,53185
1
A: Two-component response regulator 1452 receiver
hetero molecules

A: Two-component response regulator 1452 receiver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,12110
Polymers29,8782
Non-polymers2438
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation27_555-x+1/2,y,-z1
Buried area1690 Å2
ΔGint-84 kcal/mol
Surface area12390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.726, 128.726, 128.726
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132
Components on special symmetry positions
IDModelComponents
11A-362-

HOH

21A-386-

HOH

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Components

#1: Protein Two-component response regulator 1452 receiver


Mass: 14939.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. novicida (strain U112) (bacteria)
Strain: U112 / Gene: FTN_1452 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0Q7V5
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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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: 2.97 Å3/Da / Density % sol: 58.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M Calcium Chloride, 0.1 M HEPES pH 7.5, 28% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 17102 / % possible obs: 99.99 % / Redundancy: 24.7 % / CC1/2: 0.083 / Rsym value: 0.079 / Net I/σ(I): 83.425
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 8 % / Mean I/σ(I) obs: 2.205 / Num. unique all: 849 / CC1/2: 0.502 / Rsym value: 0.74 / % possible all: 99.94

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UIC

5uic


Resolution: 1.803→45.512 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.56
RfactorNum. reflection% reflection
Rfree0.2019 1711 10 %
Rwork0.1824 --
obs0.1844 17102 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.803→45.512 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms969 0 4 87 1060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005983
X-RAY DIFFRACTIONf_angle_d0.7821329
X-RAY DIFFRACTIONf_dihedral_angle_d12.691374
X-RAY DIFFRACTIONf_chiral_restr0.051160
X-RAY DIFFRACTIONf_plane_restr0.005166
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8032-1.85630.251400.24831268X-RAY DIFFRACTION100
1.8563-1.91620.22341410.2181254X-RAY DIFFRACTION100
1.9162-1.98470.21731380.18881242X-RAY DIFFRACTION100
1.9847-2.06420.20521400.17551272X-RAY DIFFRACTION100
2.0642-2.15810.19951400.17361259X-RAY DIFFRACTION100
2.1581-2.27190.20381410.18341259X-RAY DIFFRACTION100
2.2719-2.41420.18741400.18531267X-RAY DIFFRACTION100
2.4142-2.60060.24471420.18251273X-RAY DIFFRACTION100
2.6006-2.86230.20541430.19091291X-RAY DIFFRACTION100
2.8623-3.27630.18161440.19411297X-RAY DIFFRACTION100
3.2763-4.12740.17371460.17771310X-RAY DIFFRACTION100
4.1274-45.5260.21811560.17391399X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 16.9365 Å / Origin y: -13.0268 Å / Origin z: -3.286 Å
111213212223313233
T0.2881 Å20.011 Å2-0.082 Å2-0.2608 Å20.0603 Å2--0.2447 Å2
L2.7539 °20.5023 °2-0.1889 °2-1.5529 °2-0.2791 °2--3.5401 °2
S-0.0835 Å °0.1836 Å °0.2374 Å °-0.0576 Å °0.1431 Å °0.0733 Å °-0.039 Å °-0.1994 Å °-0.0199 Å °
Refinement TLS groupSelection details: all

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