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- PDB-6za3: Structure of the transcriptional repressor Atu1419 (VanR) from ag... -

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Basic information

Entry
Database: PDB / ID: 6za3
TitleStructure of the transcriptional repressor Atu1419 (VanR) from agrobacterium fabrum in complex a palindromic DNA (C2221 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
FCD / GntR, C-terminal / FCD domain / Transcription regulator FadR/GntR, C-terminal / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
ACETATE ION / DNA / Transcriptional regulator, GntR family
Similarity search - Component
Biological speciesAgrobacterium fabrum str. C58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsMorera, S. / 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 4, 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: Transcriptional regulator, GntR family
E: DNA (5'-D(*AP*TP*GP*TP*AP*TP*AP*CP*AP*T)-3')
F: DNA (5'-D(*AP*TP*GP*TP*AP*TP*AP*CP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,48012
Polymers60,9004
Non-polymers5798
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7600 Å2
ΔGint-107 kcal/mol
Surface area22630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.446, 112.402, 179.552
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-456-

HOH

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Components

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Protein / DNA chain , 2 types, 4 molecules ABEF

#1: Protein Transcriptional regulator, GntR family


Mass: 27407.182 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum str. C58 (bacteria)
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.: 2
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 , 6 types, 154 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.45 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.7 / Details: PEG 400, MES, Na-acetate

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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 EIGER2 X 9M / Detector: PIXEL / Date: Sep 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→35.07 Å / Num. obs: 43067 / % possible obs: 97.7 % / Redundancy: 8.7 % / Biso Wilson estimate: 44.19 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Net I/σ(I): 13.7
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 3095 / CC1/2: 0.421

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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: 2.05→35.07 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU R Cruickshank DPI: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.174 / SU Rfree Blow DPI: 0.154 / SU Rfree Cruickshank DPI: 0.154
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1976 5.02 %RANDOM
Rwork0.193 ---
obs0.194 39378 97.8 %-
Displacement parametersBiso max: 146.99 Å2 / Biso mean: 51.36 Å2 / Biso min: 25.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.9615 Å20 Å20 Å2
2---2.3976 Å20 Å2
3---1.4361 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: final / Resolution: 2.05→35.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3637 404 29 146 4216
Biso mean--67.01 48.06 -
Num. residues----497
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1453SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes679HARMONIC5
X-RAY DIFFRACTIONt_it4179HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion542SEMIHARMONIC5
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_contact4884SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4179HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5716HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion2.84
X-RAY DIFFRACTIONt_other_torsion17.04
LS refinement shellResolution: 2.05→2.07 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2731 45 5.71 %
Rwork0.204 743 -
all0.208 788 -
obs--70.03 %
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)
12.40860.3679-0.31531.18170.17973.3975-0.0108-0.35910.3773-0.044-0.03180.1591-0.54420.00420.04260.01350.0077-0.0441-0.023-0.0698-0.02364.4243-12.0058-6.4057
21.4583-0.01430.2342.3855-0.25581.78860.0534-0.09290.28330.1328-0.0729-0.0599-0.2296-0.00870.0195-0.0106-0.00240.0424-0.142-0.0121-0.0163-2.1347-5.4891-32.9566
31.32170.6625-0.40420.9906-0.10394.7971-0.1556-0.2975-0.1094-0.0252-0.0178-0.0820.1910.02630.1734-0.05620.00720.05330.03580.0278-0.0676-9.7736-29.0167-7.1584
42.05430.0676-0.12711.77360.39461.93170.0866-0.0685-0.33670.1034-0.1351-0.0040.2247-0.01740.04850.0048-0.005-0.0147-0.13380.0095-0.00841.2297-36.0727-32.7237
54.07260.13930.99823.40410.24213.2018-0.1123-0.54420.20130.4615-0.09540.296-0.283-0.21960.2077-0.11640.03260.02130.1802-0.0872-0.1904-4.955-19.63119.3284
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|5 - 76 }A5 - 76
2X-RAY DIFFRACTION2{ A|77 - 500 }A77 - 500
3X-RAY DIFFRACTION3{ B|5 - 76 }B5 - 76
4X-RAY DIFFRACTION4{ B|77 - 500 }B77 - 500
5X-RAY DIFFRACTION5{ E|* F|*}E1 - 10
6X-RAY DIFFRACTION5{ E|* F|*}F1 - 10

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