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

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Basic information

Entry
Database: PDB / ID: 7kua
TitleCrystal structure of the MarR family transcriptional regulator from Pseudomonas putida bound to Indole 3 acetic acid
ComponentsTranscriptional regulator, MarR family
KeywordsDNA BINDING PROTEIN / Transcriptional Regulator / Ligand Binding
Function / homology
Function and homology information


response to stress / DNA-binding transcription factor activity / DNA binding
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 / HTH-type transcriptional repressor IacR
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 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
DepositionNov 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 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: Transcriptional regulator, MarR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2962
Polymers22,1211
Non-polymers1751
Water1,04558
1
A: Transcriptional regulator, MarR family
hetero molecules

A: Transcriptional regulator, MarR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5924
Polymers44,2422
Non-polymers3502
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area7360 Å2
ΔGint-38 kcal/mol
Surface area14640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.557, 57.557, 91.384
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Transcriptional regulator, MarR family / IacR protein


Mass: 22120.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: iacR, E6B08_12615 / Production host: Escherichia coli (E. coli) / References: UniProt: B0FXI7
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 1.98 Å3/Da / Density % sol: 37.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Anatrace MCSG2 screen 35 % (v/v) Microlytic Mix(1), pH 7.0, which consists of: 1.8305 M Malonic acid, 0.25 M Ammonium citrate tribasic, 0.12 M Succinic acid, 0.3 M DL-Malic acid, 0.4 M ...Details: Anatrace MCSG2 screen 35 % (v/v) Microlytic Mix(1), pH 7.0, which consists of: 1.8305 M Malonic acid, 0.25 M Ammonium citrate tribasic, 0.12 M Succinic acid, 0.3 M DL-Malic acid, 0.4 M Sodium acetate trihydrate, 0.5 M Sodium formate, 0.16 M Ammonium tartrate dibasic, the mixture titrated to pH 7.0 using sodium hydroxide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03322 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: 1.03322 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 14591 / % possible obs: 99.9 % / Redundancy: 8.3 % / Biso Wilson estimate: 29.48 Å2 / CC1/2: 1 / Net I/σ(I): 33.4
Reflection shellResolution: 1.88→1.91 Å / Num. unique obs: 715 / CC1/2: 0.957

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CJN

3cjn


Resolution: 1.89→25.99 Å / SU ML: 0.2014 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.0325
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2158 1460 10.06 %
Rwork0.1785 13058 -
obs0.1823 14518 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.08 Å2
Refinement stepCycle: LAST / Resolution: 1.89→25.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1237 0 13 58 1308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00961312
X-RAY DIFFRACTIONf_angle_d0.91791778
X-RAY DIFFRACTIONf_chiral_restr0.3684193
X-RAY DIFFRACTIONf_plane_restr0.0052233
X-RAY DIFFRACTIONf_dihedral_angle_d23.1363504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.950.33691340.28291211X-RAY DIFFRACTION93.08
1.95-2.030.26751450.22351282X-RAY DIFFRACTION99.72
2.03-2.120.2571400.20271306X-RAY DIFFRACTION99.59
2.12-2.240.26231440.1861273X-RAY DIFFRACTION99.72
2.24-2.380.22371470.19041307X-RAY DIFFRACTION99.86
2.38-2.560.21391450.18371296X-RAY DIFFRACTION99.86
2.56-2.820.2511460.18841316X-RAY DIFFRACTION99.93
2.82-3.220.23381470.18391320X-RAY DIFFRACTION99.93
3.22-4.060.16891520.16261335X-RAY DIFFRACTION99.93
4.06-25.990.2021600.16141412X-RAY DIFFRACTION99.87

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