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- PDB-6g87: Flavonoid-responsive Regulator FrrA -

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Basic information

Entry
Database: PDB / ID: 6g87
TitleFlavonoid-responsive Regulator FrrA
ComponentsTetR/AcrR family transcriptional regulator
KeywordsTRANSCRIPTION / Flavonoids / repressor / TetR-family
Function / homology
Function and homology information


Transcriptional regulator TetR, C-terminal, Proteobacteria type / AefR-like transcriptional repressor, C-terminal domain / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeodomain-like / Homeobox-like domain superfamily ...Transcriptional regulator TetR, C-terminal, Proteobacteria type / AefR-like transcriptional repressor, C-terminal domain / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
TetR/AcrR family transcriptional regulator
Similarity search - Component
Biological speciesBradyrhizobium diazoefficiens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.92 Å
AuthorsWerner, N. / Hoppen, J. / Palm, G. / Werten, S. / Goettfert, M. / Hinrichs, W.
Citation
Journal: Febs J. / Year: 2021
Title: The induction mechanism of the flavonoid-responsive regulator FrrA.
Authors: Werner, N. / Werten, S. / Hoppen, J. / Palm, G.J. / Gottfert, M. / Hinrichs, W.
#1: Journal: Journal of Bacteriology / Year: 2012
Title: Characterization of the Flavonoid-Responsive Regulator FrrA and Its Binding Sites
Authors: Wenzel, M. / Lang, K. / Gottfert, M.
History
DepositionApr 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 18, 2021Group: Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_refine_tls_group
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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: TetR/AcrR family transcriptional regulator
B: TetR/AcrR family transcriptional regulator
C: TetR/AcrR family transcriptional regulator
D: TetR/AcrR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7938
Polymers95,9644
Non-polymers8294
Water00
1
A: TetR/AcrR family transcriptional regulator
B: TetR/AcrR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6045
Polymers47,9822
Non-polymers6223
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-4 kcal/mol
Surface area19110 Å2
MethodPISA
2
C: TetR/AcrR family transcriptional regulator
D: TetR/AcrR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1893
Polymers47,9822
Non-polymers2071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-15 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.592, 119.592, 78.476
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYALAALAAA20 - 21420 - 214
21GLYGLYALAALABB20 - 21420 - 214
12GLYGLYARGARGAA20 - 21320 - 213
22GLYGLYARGARGCC20 - 21320 - 213
13GLYGLYARGARGAA20 - 21320 - 213
23GLYGLYARGARGDD20 - 21320 - 213
14GLYGLYARGARGBB20 - 21320 - 213
24GLYGLYARGARGCC20 - 21320 - 213
15GLYGLYARGARGBB20 - 21320 - 213
25GLYGLYARGARGDD20 - 21320 - 213
16ALAALAALAALACC19 - 21419 - 214
26ALAALAALAALADD19 - 21419 - 214

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
TetR/AcrR family transcriptional regulator


Mass: 23991.004 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The sequence represents the crystallized polypeptide
Source: (gene. exp.) Bradyrhizobium diazoefficiens (bacteria)
Gene: CO678_15510
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A2A6N3G4
#2: Chemical
ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H17NO3S / Comment: pH buffer*YM
Has protein modificationY

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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: 3.2 Å3/Da / Density % sol: 61.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 6mg/ml FrrA in 20 mM Na2HPO4, 100 mM imidazole, pH 7.5, 50 mM NaCl. Precipitant 20 % PEG 8000; 0.1 M CHES, pH 9.5.
PH range: 7.5 - 9.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.979031 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979031 Å / Relative weight: 1
ReflectionResolution: 2.919→47.57 Å / Num. obs: 47028 / % possible obs: 99.6 % / Redundancy: 7.02 % / Biso Wilson estimate: 70.5 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.101 / Net I/σ(I): 15.17
Reflection shellResolution: 2.919→3.1 Å / Redundancy: 7.17 % / Mean I/σ(I) obs: 1.96 / Num. unique obs: 7487 / Rrim(I) all: 0.931 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XDSdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MAD / Resolution: 2.92→47.56 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.948 / SU B: 34.077 / SU ML: 0.276 / Cross valid method: THROUGHOUT / ESU R Free: 0.324 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21112 1080 4.5 %RANDOM
Rwork0.18252 ---
obs0.18383 23109 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 78.384 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2---0.71 Å20 Å2
3---1.42 Å2
Refinement stepCycle: 1 / Resolution: 2.92→47.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6116 0 52 0 6168
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196284
X-RAY DIFFRACTIONr_bond_other_d0.0070.026178
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.9948491
X-RAY DIFFRACTIONr_angle_other_deg1.358314171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.565778
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64823.145283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.013151037
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4961555
X-RAY DIFFRACTIONr_chiral_restr0.0760.2962
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217045
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021450
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_it3.4444.9333124
X-RAY DIFFRACTIONr_mcbond_other3.4444.9313123
X-RAY DIFFRACTIONr_mcangle_it5.297.3983898
X-RAY DIFFRACTIONr_mcangle_other5.2897.43899
X-RAY DIFFRACTIONr_scbond_it4.3675.5683160
X-RAY DIFFRACTIONr_scbond_other4.3665.5683161
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.9378.1384594
X-RAY DIFFRACTIONr_long_range_B_refined8.87739.8877089
X-RAY DIFFRACTIONr_long_range_B_other8.87739.8787087
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)
11A110130.12
12B110130.12
21A113190.1
22C113190.1
31A109160.12
32D109160.12
41B108040.13
42C108040.13
51B111890.1
52D111890.1
61C108060.13
62D108060.13
LS refinement shellResolution: 2.919→2.995 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 78 -
Rwork0.31 1671 -
obs--98.87 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.93622.0904-1.95343.3862-1.90212.14730.0534-0.2549-0.19020.0871-0.203-0.4817-0.28710.23140.14960.08020.00610.01370.1732-0.03310.138753.218533.01581.0915
21.3768-0.8221-0.09296.49641.14131.5654-0.07420.2659-0.0808-0.774-0.01430.6416-0.3716-0.2460.08860.1546-0.002-0.07120.2733-0.04840.116628.802737.5009-0.7919
32.15130.38540.05916.53752.16022.4744-0.0614-0.38080.02540.62250.06190.47770.1861-0.1773-0.00050.07190.0530.04110.19080.0090.0664-11.728324.788624.8121
44.9755-3.49830.58273.6236-0.72270.41820.01590.09640.5444-0.2803-0.173-0.2469-0.14750.08940.15710.2846-0.0556-0.07520.0789-0.0530.244510.179536.38122.2662
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 214
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION2B20 - 214
4X-RAY DIFFRACTION2A302
5X-RAY DIFFRACTION2B301
6X-RAY DIFFRACTION3C19 - 214
7X-RAY DIFFRACTION4D19 - 214
8X-RAY DIFFRACTION4D301

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