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- PDB-7l19: Crystal structure of the MarR family transcriptional regulator fr... -

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Basic information

Entry
Database: PDB / ID: 7l19
TitleCrystal structure of the MarR family transcriptional regulator from Enterobacter soli strain LF7 bound to Indole 3 acetic acid
ComponentsMarR family transcriptional regulator
KeywordsDNA BINDING PROTEIN / Transcriptional Regulator / Ligand Binding
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
1H-INDOL-3-YLACETIC ACID / NICKEL (II) ION / MarR family transcriptional regulator
Similarity search - Component
Biological speciesEnterobacter soli ATCC BAA-2102 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.77 Å
AuthorsLietzan, A.D. / Walton, W.G. / Redinbo, M.R. / Dangl, J.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)IOS-1917270 United States
CitationJournal: Nat Microbiol / Year: 2022
Title: Diverse MarR bacterial regulators of auxin catabolism in the plant microbiome.
Authors: Conway, J.M. / Walton, W.G. / Salas-Gonzalez, I. / Law, T.F. / Lindberg, C.A. / Crook, L.E. / Kosina, S.M. / Fitzpatrick, C.R. / Lietzan, A.D. / Northen, T.R. / Jones, C.D. / Finkel, O.M. / ...Authors: Conway, J.M. / Walton, W.G. / Salas-Gonzalez, I. / Law, T.F. / Lindberg, C.A. / Crook, L.E. / Kosina, S.M. / Fitzpatrick, C.R. / Lietzan, A.D. / Northen, T.R. / Jones, C.D. / Finkel, O.M. / Redinbo, M.R. / Dangl, J.L.
History
DepositionDec 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MarR family transcriptional regulator
B: MarR family transcriptional regulator
C: MarR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9447
Polymers61,3603
Non-polymers5844
Water724
1
A: MarR family transcriptional regulator
hetero molecules

A: MarR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2574
Polymers40,9072
Non-polymers3502
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_766-x+2,-x+y+1,-z+5/31
MethodPISA
2
B: MarR family transcriptional regulator
C: MarR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3165
Polymers40,9072
Non-polymers4093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.699, 117.699, 74.140
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein MarR family transcriptional regulator


Mass: 20453.318 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter soli ATCC BAA-2102 (bacteria)
Gene: M987_03643 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A198GGN0
#2: Chemical ChemComp-IAC / 1H-INDOL-3-YLACETIC ACID / INDOLE ACETIC ACID


Mass: 175.184 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris: HCl, pH 6.5, 2 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.76→50 Å / Num. obs: 15270 / % possible obs: 99.1 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.052 / Rrim(I) all: 0.164 / Χ2: 3.222 / Net I/σ(I): 7.9 / Num. measured all: 145150
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.76-2.814.51.2346820.6530.5611.3640.46590
2.81-2.865.51.0917390.6730.4591.1910.60296.6
2.86-2.916.80.9767460.8150.3781.0510.627100
2.91-2.978.10.8317460.9040.2980.8840.60298.8
2.97-3.049.30.97720.8960.3070.9520.567100
3.04-3.1110.10.8197470.9010.2680.8630.57499.1
3.11-3.199.90.6977630.9370.230.7350.602100
3.19-3.2710.10.5427620.9460.1780.5710.66999.3
3.27-3.3710.70.4177570.980.1320.4380.77299.3
3.37-3.4810.10.3827590.9790.1260.4021.382100
3.48-3.610.90.2737510.990.0860.2861.03199.5
3.6-3.7510.80.3017780.9690.0960.3162.51899.6
3.75-3.929.90.2117690.990.070.2222.14599.7
3.92-4.1210.50.1237650.9930.040.132.18599.7
4.12-4.3810.20.1187680.9910.0390.1242.57299.9
4.38-4.72110.0967800.9940.030.1012.43499.5
4.72-5.1910.30.0957630.9950.030.0993.60399.9
5.19-5.9410.40.0957860.9890.0310.13.41999.9
5.94-7.4810.50.0838000.9960.0270.0885.69100
7.48-509.80.0698370.9960.0230.07325.668100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KUA

7kua


Resolution: 2.77→46.14 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.88 / SU B: 34.484 / SU ML: 0.305 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.607 / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2762 765 5 %RANDOM
Rwork0.2333 ---
obs0.2356 14495 98.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 169.38 Å2 / Biso mean: 72.519 Å2 / Biso min: 38.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20.45 Å20 Å2
2--0.9 Å2-0 Å2
3----2.91 Å2
Refinement stepCycle: final / Resolution: 2.77→46.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2754 0 40 4 2798
Biso mean--68.34 62.33 -
Num. residues----379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132836
X-RAY DIFFRACTIONr_bond_other_d0.0030.0172628
X-RAY DIFFRACTIONr_angle_refined_deg1.9251.6573846
X-RAY DIFFRACTIONr_angle_other_deg1.5091.5875948
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2685373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.05522.703111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.27915423
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8521511
X-RAY DIFFRACTIONr_chiral_restr0.0940.2394
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023262
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02664
LS refinement shellResolution: 2.77→2.839 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.415 48 -
Rwork0.373 963 -
obs--89.39 %
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)
16.1748-3.0203-0.70322.70452.09124.62390.11150.3372-0.1595-0.31790.1463-0.29950.57851.067-0.25780.5140.24260.19880.3286-0.01360.156473.635488.926252.9205
24.4124-0.43540.73673.7977-0.54335.74380.12940.3152-0.1332-0.5619-0.15310.96140.0687-1.60310.02370.23430.0661-0.14410.5913-0.09840.2496101.063468.68943.9404
34.9512-1.9566-2.76191.79680.02934.76740.1875-0.26890.23480.12780.21490.3498-0.5362-0.9012-0.40240.19480.05610.07280.5515-0.04920.2192101.277274.506120.7864
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 201
2X-RAY DIFFRACTION2B17 - 201
3X-RAY DIFFRACTION3C17 - 201

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