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- PDB-6fi9: Crystal Structure of a zinc-responsive MarR family member, Lactoc... -

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Basic information

Entry
Database: PDB / ID: 6fi9
TitleCrystal Structure of a zinc-responsive MarR family member, Lactococcus lactis ZitR
ComponentsTranscriptional regulator ZitR
KeywordsGENE REGULATION / Zinc transport Regulator / Adhesin competence Regulator / Multiple antibiotic resistance Regulator / Zinc Responsive Repressor / winged Helix-Turn-Helix DNA binding domain
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / zinc ion binding
Similarity search - Function
Helix Hairpins - #1680 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2360 / : / : / Transcriptional regulator SarA/Rot / ArsR-like helix-turn-helix domain / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Helix Hairpins ...Helix Hairpins - #1680 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2360 / : / : / Transcriptional regulator SarA/Rot / ArsR-like helix-turn-helix domain / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Helix Hairpins / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Special / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional regulator ZitR
Similarity search - Component
Biological speciesLactococcus lactis subsp. cremoris (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsVarela, P.F. / Legrand, P.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-10-INSB-05-01 France
CitationJournal: PLoS ONE / Year: 2019
Title: Biophysical and structural characterization of a zinc-responsive repressor of the MarR superfamily.
Authors: Varela, P.F. / Velours, C. / Aumont-Nicaise, M. / Pineau, B. / Legrand, P. / Poquet, I.
History
DepositionJan 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 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 ZitR
B: Transcriptional regulator ZitR
C: Transcriptional regulator ZitR
D: Transcriptional regulator ZitR
E: Transcriptional regulator ZitR
F: Transcriptional regulator ZitR
G: Transcriptional regulator ZitR
H: Transcriptional regulator ZitR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,50724
Polymers130,4618
Non-polymers1,04716
Water00
1
A: Transcriptional regulator ZitR
B: Transcriptional regulator ZitR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8776
Polymers32,6152
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-119 kcal/mol
Surface area16430 Å2
MethodPISA
2
C: Transcriptional regulator ZitR
D: Transcriptional regulator ZitR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8776
Polymers32,6152
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-122 kcal/mol
Surface area16540 Å2
MethodPISA
3
E: Transcriptional regulator ZitR
F: Transcriptional regulator ZitR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8776
Polymers32,6152
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-124 kcal/mol
Surface area17050 Å2
MethodPISA
4
G: Transcriptional regulator ZitR
H: Transcriptional regulator ZitR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8776
Polymers32,6152
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-124 kcal/mol
Surface area16640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.520, 128.520, 88.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
Transcriptional regulator ZitR


Mass: 16307.568 Da / Num. of mol.: 8 / Mutation: S2A, A4R, D8E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria)
Strain: MG1363 / Gene: zitR, llmg_2401 / Plasmid: pVE8073 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A2RNS2
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn

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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: 2.78 Å3/Da / Density % sol: 55.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M sodium citrate tribasic dihydrate 30 % polyethyleneglycol 4.000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.28189 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28189 Å / Relative weight: 1
ReflectionResolution: 3.09→48.11 Å / Num. obs: 26339 / % possible obs: 99.6 % / Redundancy: 8.9 % / Biso Wilson estimate: 102.89 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06722 / Rrim(I) all: 0.09506 / Net I/av σ(I): 12.7 / Net I/σ(I): 12.7
Reflection shellResolution: 3.09→3.17 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 1860 / CC1/2: 0.597 / % possible all: 96

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→48.15 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.881 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.516
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1028 4.75 %RANDOM
Rwork0.236 ---
obs0.237 21630 60.9 %-
Displacement parametersBiso max: 300 Å2 / Biso mean: 162.16 Å2 / Biso min: 46.37 Å2
Baniso -1Baniso -2Baniso -3
1-3.5687 Å20 Å20 Å2
2--3.5687 Å20 Å2
3----7.1373 Å2
Refine analyzeLuzzati coordinate error obs: 0.58 Å
Refinement stepCycle: final / Resolution: 2.8→48.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9152 0 16 0 9168
Biso mean--160.59 --
Num. residues----1152
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3456SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1576HARMONIC5
X-RAY DIFFRACTIONt_it9264HARMONIC20
X-RAY DIFFRACTIONt_nbd6SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1288SEMIHARMONIC5
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_contact10280SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d9264HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg12480HARMONIC21.02
X-RAY DIFFRACTIONt_omega_torsion1.72
X-RAY DIFFRACTIONt_other_torsion20.57
LS refinement shellResolution: 2.8→2.94 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.1714 12 4.71 %
Rwork0.2309 243 -
all0.2281 255 -
obs--5.53 %
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)
13.113-1.2881.22210.527-0.52473.09070.01870.0288-0.52080.12140.12110.19570.31020.1059-0.1398-0.0222-0.11690.0265-0.2985-0.0164-0.298755.298846.472931.3868
20.6115-1.1355-1.70762.15270.8254.1056-0.0045-0.04390.12860.09230.1488-0.34780.17250.3618-0.1442-0.304-0.0381-0.0547-0.27570.0138-0.30417.79478.8362-7.1437
38.1107-1.8796-1.59638.25072.12020.64340.04890.0401-0.37660.12290.0017-0.36980.48440.4656-0.05060.304-0.152-0.03680.28710.1520.30434.256816.605642.673
48.3155-2.78222.84594.9015-2.89461.6613-0.0239-0.0081-0.35470.43450.1969-0.54420.51890.5162-0.1730.304-0.1477-0.00990.3040.1520.30444.679135.596671.2748
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* B|* }A2 - 145
2X-RAY DIFFRACTION1{ A|* B|* }B2 - 145
3X-RAY DIFFRACTION2{ C|* D|* }C2 - 145
4X-RAY DIFFRACTION2{ C|* D|* }D2 - 145
5X-RAY DIFFRACTION3{ E|* F|* }E2 - 145
6X-RAY DIFFRACTION3{ E|* F|* }F2 - 145
7X-RAY DIFFRACTION4{ G|* H|* }G2 - 145
8X-RAY DIFFRACTION4{ G|* H|* }H2 - 145

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