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- PDB-6br7: Beryllium fluorinated receiver domain of BfmR from Acinetobacter ... -

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Basic information

Entry
Database: PDB / ID: 6br7
TitleBeryllium fluorinated receiver domain of BfmR from Acinetobacter baumannii
ComponentsBfmR
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 / 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 profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / 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 / Response regulator / Winged helix-like DNA-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BERYLLIUM TRIFLUORIDE ION / Two-component system response regulator protein / BfmR
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsMilton, M.E. / Cavanagh, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1 GM055769 United States
V Foundation for Cancer Research United States
CitationJournal: J. Mol. Biol. / Year: 2018
Title: The Structure of the Biofilm-controlling Response Regulator BfmR from Acinetobacter baumannii Reveals Details of Its DNA-binding Mechanism.
Authors: Draughn, G.L. / Milton, M.E. / Feldmann, E.A. / Bobay, B.G. / Roth, B.M. / Olson, A.L. / Thompson, R.J. / Actis, L.A. / Davies, C. / Cavanagh, J.
History
DepositionNov 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 28, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Feb 19, 2020Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene ..._entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.5Oct 4, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BfmR
B: BfmR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4126
Polymers30,2312
Non-polymers1814
Water6,846380
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-8 kcal/mol
Surface area12180 Å2
Unit cell
Length a, b, c (Å)52.163, 52.163, 197.566
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein BfmR / Chemotaxis protein CheY / DNA-binding response regulator / Response regulator / Transcriptional ...Chemotaxis protein CheY / DNA-binding response regulator / Response regulator / Transcriptional regulatory protein RstA / Two-component regulatory system response regulator / Two-component system response regulator protein


Mass: 15115.442 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: bfmR, rstA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2VSW6, UniProt: A0A014C6J9*PLUS
#2: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 2.77 Å3/Da / Density % sol: 55.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.6 M ammonium sulfate, 0.1 M MES pH 6.5, 10% 1,4-dioxane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.86→44.038 Å / Num. obs: 24771 / % possible obs: 97.14 % / Redundancy: 6.1 % / Rsym value: 0.091 / Net I/σ(I): 5.49
Reflection shellResolution: 1.86→1.89 Å / Rsym value: 0.173

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HM6

5hm6


Resolution: 1.86→44.038 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 17.23
RfactorNum. reflection% reflection
Rfree0.178 1998 8.09 %
Rwork0.1491 --
obs0.1515 24686 97.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.86→44.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1959 0 10 380 2349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031987
X-RAY DIFFRACTIONf_angle_d0.592688
X-RAY DIFFRACTIONf_dihedral_angle_d14.106792
X-RAY DIFFRACTIONf_chiral_restr0.046321
X-RAY DIFFRACTIONf_plane_restr0.004352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8601-1.90660.22361370.17411572X-RAY DIFFRACTION96
1.9066-1.95810.2341380.16241575X-RAY DIFFRACTION94
1.9581-2.01570.1911440.15171598X-RAY DIFFRACTION96
2.0157-2.08080.19871370.14651619X-RAY DIFFRACTION97
2.0808-2.15520.18011430.14961621X-RAY DIFFRACTION97
2.1552-2.24150.16991420.14531596X-RAY DIFFRACTION97
2.2415-2.34350.18011430.14411631X-RAY DIFFRACTION97
2.3435-2.4670.17461430.14121632X-RAY DIFFRACTION98
2.467-2.62160.20131460.15291646X-RAY DIFFRACTION98
2.6216-2.82390.15631400.15431618X-RAY DIFFRACTION98
2.8239-3.1080.18471440.14911656X-RAY DIFFRACTION99
3.108-3.55760.17861410.14781659X-RAY DIFFRACTION99
3.5576-4.48150.13681530.12891642X-RAY DIFFRACTION98
4.4815-44.05030.19021470.16711623X-RAY DIFFRACTION96

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