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

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Basic information

Entry
Database: PDB / ID: 6nwo
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
beta-lactose / 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 / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _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
D: Transcriptional regulator BgaR
B: Transcriptional regulator BgaR
C: Transcriptional regulator BgaR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4637
Polymers84,9934
Non-polymers4703
Water2,666148
1
A: Transcriptional regulator BgaR
D: Transcriptional regulator BgaR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8393
Polymers42,4962
Non-polymers3421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-10 kcal/mol
Surface area15280 Å2
MethodPISA
2
B: Transcriptional regulator BgaR
C: Transcriptional regulator BgaR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6244
Polymers42,4962
Non-polymers1282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-20 kcal/mol
Surface area15090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.429, 40.482, 261.721
Angle α, β, γ (deg.)90.00, 90.33, 90.00
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12A
22B
13A
23C
14D
24B
15D
25C
16B
26C

NCS domain segments:

Component-ID: _ / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSAA10 - 16010 - 160
21LYSLYSDB10 - 16010 - 160
12GLUGLUAA11 - 16011 - 160
22GLUGLUBC11 - 16011 - 160
13LYSLYSAA10 - 16010 - 160
23LYSLYSCD10 - 16010 - 160
14GLUGLUDB11 - 16011 - 160
24GLUGLUBC11 - 16011 - 160
15ILEILEDB3 - 1603 - 160
25ILEILECD3 - 1603 - 160
16GLUGLUBC11 - 16011 - 160
26GLUGLUCD11 - 16011 - 160

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Transcriptional regulator BgaR


Mass: 21248.188 Da / Num. of mol.: 4
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-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#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.: 148 / 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: 2.13 Å3/Da / Density % sol: 42.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: 5 mg/mL protein; 21.7% PEG 3350, 222mM MgCl2, 100mM bis-tris pH 5.7. Sitting drops were set up in 200 nL plus 200 nL volumes 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: 2.11→43.62 Å / Num. obs: 41261 / % possible obs: 98.7 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.043 / Net I/σ(I): 9.4
Reflection shellResolution: 2.11→2.17 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.672 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3104 / CC1/2: 0.744 / Rpim(I) all: 0.29 / % possible all: 91.7

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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→43.6 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.215 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.183 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2305 2066 5 %RANDOM
Rwork0.19376 ---
obs0.19559 39182 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.041 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å2-0 Å2-0.21 Å2
2--2.97 Å20 Å2
3----1.87 Å2
Refinement stepCycle: 1 / Resolution: 2.11→43.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5036 0 30 148 5214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135253
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174707
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.6427138
X-RAY DIFFRACTIONr_angle_other_deg1.3341.57510999
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.495639
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.4825.31258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.25315896
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.453158
X-RAY DIFFRACTIONr_chiral_restr0.0730.2683
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025855
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021045
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_it3.2164.0312544
X-RAY DIFFRACTIONr_mcbond_other3.214.0292543
X-RAY DIFFRACTIONr_mcangle_it4.5326.0283187
X-RAY DIFFRACTIONr_mcangle_other4.5326.0313188
X-RAY DIFFRACTIONr_scbond_it4.3564.572709
X-RAY DIFFRACTIONr_scbond_other4.3564.5712710
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7046.663952
X-RAY DIFFRACTIONr_long_range_B_refined9.17676.90521313
X-RAY DIFFRACTIONr_long_range_B_other9.17576.93521250
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A48900.08
12D48900.08
21A48610.09
22B48610.09
31A48630.1
32C48630.1
41D48090.08
42B48090.08
51D50260.09
52C50260.09
61B48660.08
62C48660.08
LS refinement shellResolution: 2.113→2.168 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 131 -
Rwork0.26 2652 -
obs--91.31 %

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