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- PDB-6nwm: Structures of the transcriptional regulator BgaR, a lactose sensor. -

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Basic information

Entry
Database: PDB / ID: 6nwm
TitleStructures of the transcriptional regulator BgaR, a lactose sensor.
ComponentsTranscriptional regulator BgaR
KeywordsTRANSCRIPTION / lactose transcriptional regulator / lactose sensor / SAD phasing
Function / homology
Function and homology information


sequence-specific DNA binding / DNA-binding transcription factor activity
Similarity search - Function
Regulatory protein AraC / Transcription regulator HTH-like / AraC-type arabinose-binding/dimerisation domain / AraC-like ligand binding domain / Transcription regulator HTH, AraC- type / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / Helix-turn-helix domain / DNA binding HTH domain, AraC-type / Bacterial regulatory proteins, araC family DNA-binding domain profile. ...Regulatory protein AraC / Transcription regulator HTH-like / AraC-type arabinose-binding/dimerisation domain / AraC-like ligand binding domain / Transcription regulator HTH, AraC- type / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / Helix-turn-helix domain / DNA binding HTH domain, AraC-type / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Homeobox-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
lactulose / Probable transcriptional regulator
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsPeat, T.S. / Newman, J.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Structures of the transcriptional regulator BgaR, a lactose sensor.
Authors: Newman, J. / Caron, K. / Nebl, T. / Peat, T.S.
History
DepositionFeb 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator BgaR
B: Transcriptional regulator BgaR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1814
Polymers42,4962
Non-polymers6852
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-7 kcal/mol
Surface area15300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.439, 87.528, 118.974
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 1 - 162 / Label seq-ID: 1 - 162

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Transcriptional regulator BgaR


Mass: 21248.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (strain 13 / Type A) (bacteria)
Strain: 13 / Type A / Gene: CPE0770 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8XMB9
#2: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-fructofuranose / lactulose


Type: oligosaccharide, Oligosaccharide / Class: Water retention / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: lactulose
DescriptorTypeProgram
DGalpb1-4DFrufb2-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.84 Å3/Da / Density % sol: 56.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 5 mg/mL protein; 1.27 M sodium malonate, 100 mM HEPES pH 7.5. Sitting drops were set up in 200 nL plus 200 nL volumes with seeds at 20C

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953723 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953723 Å / Relative weight: 1
ReflectionResolution: 1.94→46.4 Å / Num. obs: 36663 / % possible obs: 99.8 % / Redundancy: 13.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.048 / Net I/σ(I): 9.4
Reflection shellResolution: 1.94→1.99 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.776 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2389 / CC1/2: 0.761 / Rpim(I) all: 0.498 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6nwh

6nwh


Resolution: 2.11→43.8 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.811 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.132 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23324 1776 4.9 %RANDOM
Rwork0.20378 ---
obs0.20523 34833 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.343 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å2-0 Å2
2--2.81 Å2-0 Å2
3----3.6 Å2
Refinement stepCycle: 1 / Resolution: 2.11→43.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2625 0 46 133 2804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132808
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172536
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.6453823
X-RAY DIFFRACTIONr_angle_other_deg1.3061.5725941
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0015338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.57125.373134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.8915491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.169154
X-RAY DIFFRACTIONr_chiral_restr0.0730.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023086
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02550
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6463.3781334
X-RAY DIFFRACTIONr_mcbond_other2.6473.3761333
X-RAY DIFFRACTIONr_mcangle_it3.8395.0391678
X-RAY DIFFRACTIONr_mcangle_other3.8385.0421679
X-RAY DIFFRACTIONr_scbond_it3.7433.9151474
X-RAY DIFFRACTIONr_scbond_other3.7423.9161475
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9215.72146
X-RAY DIFFRACTIONr_long_range_B_refined7.95865.30611624
X-RAY DIFFRACTIONr_long_range_B_other7.9665.27711564
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 5378 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 130 -
Rwork0.365 2501 -
obs--99.28 %

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