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- PDB-6g8g: Flavonoid-responsive Regulator FrrA in complex with Genistein -

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Basic information

Entry
Database: PDB / ID: 6g8g
TitleFlavonoid-responsive Regulator FrrA in complex with Genistein
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
GENISTEIN / TetR/AcrR family transcriptional regulator
Similarity search - Component
Biological speciesBradyrhizobium diazoefficiens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 18, 2021Group: Database references / Category: citation / citation_author / database_2
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 1.2Jan 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)97,95613
Polymers95,9644
Non-polymers1,9929
Water00
1
A: TetR/AcrR family transcriptional regulator
B: TetR/AcrR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2898
Polymers47,9822
Non-polymers1,3076
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: TetR/AcrR family transcriptional regulator
D: TetR/AcrR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6675
Polymers47,9822
Non-polymers6853
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.044, 119.044, 78.305
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
11GLYGLYPROPROAA20 - 21220 - 212
21GLYGLYPROPROBB20 - 21220 - 212
12ALAALAARGARGAA19 - 21319 - 213
22ALAALAARGARGCC19 - 21319 - 213
13ALAALAARGARGAA19 - 21319 - 213
23ALAALAARGARGDD19 - 21319 - 213
14GLYGLYPROPROBB20 - 21220 - 212
24GLYGLYPROPROCC20 - 21220 - 212
15GLYGLYPROPROBB20 - 21220 - 212
25GLYGLYPROPRODD20 - 21220 - 212
16ALAALAARGARGCC19 - 21319 - 213
26ALAALAARGARGDD19 - 21319 - 213

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(DE3) (bacteria) / Variant (production host): Gold pLysS AG / References: UniProt: A0A2A6N3G4
#2: Chemical
ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Chemical ChemComp-GEN / GENISTEIN / 5,7-DIHYDROXY-3-(4-HYDROXYPHENYL)-4H-1-BENZOPYRAN-4-ONE / 4',5,7-TRIHYDROXYISOFLAVONE / PRUNETOL / GENISTEOL


Mass: 270.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H10O5
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: 2.89 Å3/Da / Density % sol: 57.45 %
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 with equimolar Genistein in 70% Ethanol. 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: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.599→119.1 Å / Num. obs: 65566 / % possible obs: 99.1 % / Redundancy: 3.44 % / Biso Wilson estimate: 76.3 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.091 / Net I/σ(I): 11.52
Reflection shellResolution: 2.599→2.7 Å / Redundancy: 3.35 % / Mean I/σ(I) obs: 0.82 / Num. unique obs: 10480 / CC1/2: 0.279 / Rrim(I) all: 1.52 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G87

6g87


Resolution: 2.6→119.04 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 28.664 / SU ML: 0.245 / Cross valid method: THROUGHOUT / ESU R: 0.467 / ESU R Free: 0.253 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21644 1719 5.1 %RANDOM
Rwork0.18839 ---
obs0.18984 32099 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 75.677 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å2-0 Å20 Å2
2---0.72 Å20 Å2
3---1.43 Å2
Refinement stepCycle: 1 / Resolution: 2.6→119.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6115 0 131 0 6246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196366
X-RAY DIFFRACTIONr_bond_other_d0.0070.026258
X-RAY DIFFRACTIONr_angle_refined_deg1.6782.0078598
X-RAY DIFFRACTIONr_angle_other_deg1.438314358
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4775775
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5423.007286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.295151046
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5351558
X-RAY DIFFRACTIONr_chiral_restr0.0840.2965
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217076
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021476
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_it4.1075.6493112
X-RAY DIFFRACTIONr_mcbond_other4.1045.6463111
X-RAY DIFFRACTIONr_mcangle_it6.0238.4713883
X-RAY DIFFRACTIONr_mcangle_other6.0228.4733884
X-RAY DIFFRACTIONr_scbond_it6.1286.5933254
X-RAY DIFFRACTIONr_scbond_other6.1276.5933255
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.589.5764716
X-RAY DIFFRACTIONr_long_range_B_refined11.37946.657131
X-RAY DIFFRACTIONr_long_range_B_other11.3846.6437129
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)
11A105760.13
12B105760.13
21A115130.08
22C115130.08
31A108000.12
32D108000.12
41B107730.13
42C107730.13
51B116110.09
52D116110.09
61C107910.13
62D107910.13
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.46 93 -
Rwork0.417 2333 -
obs--97.43 %
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)
11.65940.51820.66070.94120.4830.3770.0722-0.01050.10120.1013-0.11930.11050.0937-0.01570.04710.13180.0094-0.03540.1463-0.0030.06286.266526.61583.7028
20.5382-0.66870.20232.7301-0.69780.466-0.00030.03420.1022-0.294-0.0493-0.28670.19330.06460.04960.11930.01940.02710.18810.04270.05530.596621.9741.7208
30.60570.5232-0.20791.9173-0.89820.4580-0.1441-0.0550.1908-0.0241-0.1703-0.1291-0.01110.0240.11050.04060.01130.17830.01940.105271.203935.060427.1964
41.8345-1.0007-0.07520.96720.03220.01410.0395-0.1519-0.1139-0.2221-0.05810.04880.0182-0.01720.01860.15190.0031-0.02870.14150.01980.10349.375323.457824.6723
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 1004
2X-RAY DIFFRACTION2B20 - 1008
3X-RAY DIFFRACTION3C19 - 1006
4X-RAY DIFFRACTION4D19 - 1005

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