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- PDB-6z74: Structure of the transcriptional repressor Atu1419 (VanR) in comp... -

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Basic information

Entry
Database: PDB / ID: 6z74
TitleStructure of the transcriptional repressor Atu1419 (VanR) in complex with a fortuitous citrate from agrobacterium fabrum
ComponentsTranscriptional regulator, GntR family
KeywordsTRANSCRIPTION / Transcriptional 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 / Transcriptional regulator, GntR family
Similarity search - Component
Biological speciesAgrobacterium fabrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsMorera, S. / Vigouroux, V.
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
DepositionMay 29, 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 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
C: Transcriptional regulator, GntR family
D: Transcriptional regulator, GntR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,42740
Polymers109,6294
Non-polymers2,79836
Water6,918384
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17640 Å2
ΔGint-87 kcal/mol
Surface area36530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.170, 113.660, 130.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Transcriptional regulator, GntR family


Mass: 27407.182 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria)
Gene: Atu1419 / Production host: Escherichia coli (E. coli) / References: UniProt: A9CJ36

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Non-polymers , 8 types, 420 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.61 Å3/Da / Density % sol: 52.89 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, AS, Na-citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2→45.64 Å / Num. obs: 78344 / % possible obs: 99.6 % / Redundancy: 5.9 % / Biso Wilson estimate: 38.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.054 / Net I/σ(I): 10
Reflection shellResolution: 2→2.12 Å / Num. unique obs: 12280 / CC1/2: 0.981

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2→45.64 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.936 / SU R Cruickshank DPI: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.159 / SU Rfree Blow DPI: 0.136 / SU Rfree Cruickshank DPI: 0.136
RfactorNum. reflection% reflectionSelection details
Rfree0.215 3915 5 %RANDOM
Rwork0.193 ---
obs0.194 78286 99.8 %-
Displacement parametersBiso mean: 53.39 Å2
Baniso -1Baniso -2Baniso -3
1-5.1426 Å20 Å20 Å2
2---12.8613 Å20 Å2
3---7.7187 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: 1 / Resolution: 2→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7202 0 168 384 7754
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017478HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9910050HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2718SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1319HARMONIC5
X-RAY DIFFRACTIONt_it7478HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.76
X-RAY DIFFRACTIONt_other_torsion16.43
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion952SEMIHARMONIC5
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_contact9075SEMIHARMONIC4
LS refinement shellResolution: 2→2.01 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2645 -4.98 %
Rwork0.2807 1488 -
all0.2798 1566 -
obs--95.1 %
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)
14.48641.41651.48892.20580.51513.7744-0.17960.5442-0.0567-0.30360.0774-0.0434-0.06140.18960.1021-0.06330.0133-0.0297-0.01680.0595-0.0787-14.045921.772262.8202
21.35430.2151-0.05011.7178-0.48061.1722-0.02630.1378-0.0095-0.2234-0.0059-0.08660.11810.06910.0322-0.05960.00450.0270.01320.0089-0.07925.049112.021580.7882
33.8213-0.90162.58593.874-1.4854.3970.1386-0.1303-0.0816-0.09030.02310.3930.117-0.5442-0.1618-0.1005-0.0667-0.0280.0191-0.0137-0.1204-28.14378.029870.7747
42.20611.17750.60061.773-0.19582.25250.0781-0.3350.19450.0916-0.0340.2345-0.089-0.5442-0.0441-0.18080.03820.00780.1070.0095-0.1221-21.123314.467297.4006
54.2258-1.54621.15853.0358-0.3845.0211-0.0424-0.54420.05060.54420.00190.1596-0.218-0.17890.04050.0916-0.0539-0.1257-0.0665-0.037-0.183312.118417.5553136.207
62.96050.39881.06971.54590.30724.3247-0.0156-0.45150.18240.2921-0.04570.151-0.1026-0.54420.0614-0.1275-0.00460.0318-0.04060.0265-0.193-8.14938.5615117.671
72.1219-0.94781.51970.512-0.14574.84430.07960.47350.0727-0.1093-0.2754-0.2351-0.06380.47260.1958-0.03210.0226-0.10020.03650.1394-0.130125.53433.4233126.519
82.611-0.94290.24861.71930.03682.6148-0.07710.33130.29250.0559-0.0263-0.3071-0.1590.54420.1034-0.2093-0.11-0.03740.11150.0708-0.134618.199114.0558101.552
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|5 - A|76 }
2X-RAY DIFFRACTION2{ A|77 - A|500 }
3X-RAY DIFFRACTION3{ B|5 - B|76 }
4X-RAY DIFFRACTION4{ B|77 - B|500 }
5X-RAY DIFFRACTION5{ C|5 - C|76 }
6X-RAY DIFFRACTION6{ C|77 - C|500 }
7X-RAY DIFFRACTION7{ D|5 - D|76 }
8X-RAY DIFFRACTION8{ D|77 - D|500 }

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