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- PDB-7l1i: Crystal structure of the MarR family transcriptional regulator fr... -

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Basic information

Entry
Database: PDB / ID: 7l1i
TitleCrystal structure of the MarR family transcriptional regulator from Acineotobacter baumannii bound to Indole 3 acetic acid
ComponentsMarR family multidrug resistance pump 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-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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
1H-INDOL-3-YLACETIC ACID / NICKEL (II) ION / MarR family multidrug resistance pump transcriptional regulator
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsWalton, W.G. / Lietzan, A.D. / 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 1.0Feb 9, 2022Provider: 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 multidrug resistance pump transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3623
Polymers20,1281
Non-polymers2342
Water1629
1
A: MarR family multidrug resistance pump transcriptional regulator
hetero molecules

A: MarR family multidrug resistance pump transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7236
Polymers40,2562
Non-polymers4684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area8960 Å2
ΔGint-73 kcal/mol
Surface area16600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.672, 72.672, 125.125
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein MarR family multidrug resistance pump transcriptional regulator


Mass: 20127.865 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: marR_1, NCTC13305_00397 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A334T093
#2: Chemical ChemComp-IAC / 1H-INDOL-3-YLACETIC ACID / INDOLE ACETIC ACID


Mass: 175.184 Da / Num. of mol.: 1 / 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.37 Å3/Da / Density % sol: 48.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M CHES: NaOH, pH 9.5, 30 % (w/v) PEG 3000

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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 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 8439 / % possible obs: 96.8 % / Redundancy: 14.4 % / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.026 / Rrim(I) all: 0.105 / Χ2: 2.271 / Net I/σ(I): 7.1 / Num. measured all: 121829
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.395.10.7343210.7820.3330.810.52377.5
2.39-2.435.70.5823640.8320.250.6360.4983.1
2.43-2.486.90.5053580.8870.1940.5420.55588.2
2.48-2.5380.463890.9150.1660.490.53192
2.53-2.599.70.464040.940.1510.4850.56394.6
2.59-2.6511.30.4344120.9490.1290.4540.5699.3
2.65-2.7114.20.3584200.9740.0970.3710.602100
2.71-2.7915.90.3244370.9790.0820.3350.664100
2.79-2.8717.80.2634240.9890.0640.2710.748100
2.87-2.9618.20.2654230.9860.0630.2730.76199.8
2.96-3.0717.10.2024260.9860.050.2081.072100
3.07-3.1917.60.1734250.990.0420.1781.366100
3.19-3.3316.90.1444340.9920.0360.1491.515100
3.33-3.5118.10.1234340.9970.0290.1261.578100
3.51-3.7317.20.1074320.9940.0270.1112.572100
3.73-4.0217.10.14480.9910.0250.1032.732100
4.02-4.4217.50.0854350.9970.020.0873.20699.5
4.42-5.0616.70.0834580.9980.0210.0853.627100
5.06-6.3716.90.0794670.9950.0190.0814.016100
6.37-5014.50.0835280.9960.0220.08610.53100

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Phasing

PhasingMethod: molecular replacement

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Processing

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

7kua


Resolution: 2.35→36.36 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU B: 21.49 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.379 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2586 404 4.8 %RANDOM
Rwork0.214 ---
obs0.216 7995 96.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 149.42 Å2 / Biso mean: 63.626 Å2 / Biso min: 38.31 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å2-0.52 Å2-0 Å2
2---1.04 Å20 Å2
3---3.39 Å2
Refinement stepCycle: final / Resolution: 2.35→36.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1329 0 14 9 1352
Biso mean--50.95 60.56 -
Num. residues----169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131376
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171340
X-RAY DIFFRACTIONr_angle_refined_deg1.7871.6451864
X-RAY DIFFRACTIONr_angle_other_deg1.5331.5853088
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2245170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.9762564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.58215255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.505154
X-RAY DIFFRACTIONr_chiral_restr0.0860.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021545
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02299
LS refinement shellResolution: 2.351→2.412 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 23 -
Rwork0.302 473 -
all-496 -
obs--78.61 %
Refinement TLS params.Method: refined / Origin x: 27.2324 Å / Origin y: 34.3658 Å / Origin z: 54.1918 Å
111213212223313233
T0.017 Å20.0088 Å2-0.0489 Å2-0.0843 Å2-0.04 Å2--0.1798 Å2
L2.2347 °20.2044 °20.4607 °2-4.2265 °21.1087 °2--1.4891 °2
S-0.0923 Å °-0.1496 Å °0.2928 Å °-0.0901 Å °-0.1606 Å °0.1126 Å °-0.1283 Å °-0.1073 Å °0.2529 Å °

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