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- PDB-6zab: Structure of the transcriptional repressor Atu1419 (VanR) from ag... -

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Basic information

Entry
Database: PDB / ID: 6zab
TitleStructure of the transcriptional repressor Atu1419 (VanR) from agrobacterium fabrum in complex a palindromic DNA (P6422 space group)
Components
  • DNA (5'-D(*AP*TP*GP*TP*AP*TP*AP*CP*AP*T)-3')
  • Transcriptional regulator, GntR family
KeywordsTRANSCRIPTION / repressor
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / metal ion binding
Similarity search - Function
GntR ligand-binding domain-like / FCD / GntR, C-terminal / FCD domain / Transcription regulator FadR/GntR, C-terminal / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Four Helix Bundle (Hemerythrin (Met), subunit A) ...GntR ligand-binding domain-like / FCD / GntR, C-terminal / FCD domain / Transcription regulator FadR/GntR, C-terminal / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Four Helix Bundle (Hemerythrin (Met), subunit A) / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CITRIC ACID / DI(HYDROXYETHYL)ETHER / DNA / Transcriptional regulator, GntR family
Similarity search - Component
Biological speciesAgrobacterium fabrum (bacteria)
Agrobacterium fabrum str. C58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsMorera, S. / Naretto, A. / Vigouroux, A. / Legrand, P.
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Characterization of the first tetrameric transcription factor of the GntR superfamily with allosteric regulation from the bacterial pathogen Agrobacterium fabrum.
Authors: Vigouroux, A. / Meyer, T. / Naretto, A. / Legrand, P. / Aumont-Nicaise, M. / Di Cicco, A. / Renoud, S. / Dore, J. / Levy, D. / Vial, L. / Lavire, C. / Morera, S.
History
DepositionJun 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 20, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator, GntR family
B: DNA (5'-D(*AP*TP*GP*TP*AP*TP*AP*CP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8766
Polymers30,4502
Non-polymers4264
Water41423
1
A: Transcriptional regulator, GntR family
B: DNA (5'-D(*AP*TP*GP*TP*AP*TP*AP*CP*AP*T)-3')
hetero molecules

A: Transcriptional regulator, GntR family
B: DNA (5'-D(*AP*TP*GP*TP*AP*TP*AP*CP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,75212
Polymers60,9004
Non-polymers8518
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/31
Buried area7220 Å2
ΔGint-93 kcal/mol
Surface area23040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.180, 179.180, 96.740
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

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Protein / DNA chain , 2 types, 2 molecules AB

#1: Protein Transcriptional regulator, GntR family


Mass: 27407.182 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria)
Strain: C58 / ATCC 33970 / Gene: Atu1419 / Production host: Escherichia coli (E. coli) / References: UniProt: A9CJ36
#2: DNA chain DNA (5'-D(*AP*TP*GP*TP*AP*TP*AP*CP*AP*T)-3')


Mass: 3043.029 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum str. C58 (bacteria)
Production host: synthetic construct (others)

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Non-polymers , 5 types, 27 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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

Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: Terbutanol, Na-citrate, MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→45.61 Å / Num. obs: 23104 / % possible obs: 99.7 % / Redundancy: 19.5 % / Biso Wilson estimate: 101.64 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.137 / Net I/σ(I): 14.3
Reflection shellResolution: 2.8→2.87 Å / Num. unique obs: 1635 / CC1/2: 0.388

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Z74

6z74


Resolution: 2.8→45.61 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.932 / SU R Cruickshank DPI: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.304 / SU Rfree Blow DPI: 0.222 / SU Rfree Cruickshank DPI: 0.222
RfactorNum. reflection% reflectionSelection details
Rfree0.199 817 5 %RANDOM
Rwork0.188 ---
obs0.189 16349 70.8 %-
Displacement parametersBiso max: 222 Å2 / Biso mean: 83.94 Å2 / Biso min: 18.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.9199 Å20 Å20 Å2
2--0.9199 Å20 Å2
3----1.8398 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: final / Resolution: 2.8→45.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1821 202 25 23 2071
Biso mean--111.22 55.67 -
Num. residues----249
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d737SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes345HARMONIC5
X-RAY DIFFRACTIONt_it2107HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion273SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2468SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2107HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg2883HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion2.22
X-RAY DIFFRACTIONt_other_torsion19.46
LS refinement shellResolution: 2.8→2.91 Å / Rfactor Rfree error: 0 / Total num. of bins used: 40
RfactorNum. reflection% reflection
Rfree0.3083 19 4.65 %
Rwork0.2596 390 -
all0.2618 409 -
obs--16.4 %
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)
13.34490.83591.27321.00640.84533.53340.0010.2948-0.53010.01880.0851-0.17030.4430.3212-0.0862-0.2423-0.10190.0989-0.1361-0.03580.264-26.12870.5865-18.0204
28.87350.7898-3.31353.9051-0.08178.31550.23440.0738-0.6649-0.4387-0.08910.1970.1306-0.0218-0.1453-0.1850.0587-0.1559-0.0468-0.02660.047-6.087590.4291-9.4147
33.3586-2.0028-2.61846.9864-1.28564.30590.2061-0.26350.62290.24310.002-0.2688-0.25860.4283-0.2081-0.1208-0.07280.05510.1471-0.0998-0.12232.6567104.2834-15.6354
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|73 - 502 }A73 - 502
2X-RAY DIFFRACTION2{ A|6 - 72 }A6 - 72
3X-RAY DIFFRACTION3{ B|* }B1 - 10

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