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- PDB-7dvn: Crystal structure of a MarR family protein in complex with a lipi... -

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Entry
Database: PDB / ID: 7dvn
TitleCrystal structure of a MarR family protein in complex with a lipid-like effector molecule from the psychrophilic bacterium Paenisporosarcina sp. TG-14
ComponentsMarR family transcriptional regulator
KeywordsDNA BINDING PROTEIN / Transcription regulator DNA-binding Complex Lipid-like effector MarR family
Function / homologyPALMITIC ACID
Function and homology information
Biological speciesPaenisporosarcina sp. TG-14 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsLee, C.W. / Hwang, J. / Do, H. / Lee, J.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)15250103 Korea, Republic Of
CitationJournal: Iucrj / Year: 2021
Title: Crystal structure of a MarR family protein from the psychrophilic bacterium Paenisporosarcina sp. TG-14 in complex with a lipid-like molecule.
Authors: Hwang, J. / Park, S.H. / Lee, C.W. / Do, H. / Shin, S.C. / Kim, H.W. / Lee, S.G. / Park, H.H. / Kwon, S. / Lee, J.H.
History
DepositionJan 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MarR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1942
Polymers16,9381
Non-polymers2561
Water2,576143
1
A: MarR family transcriptional regulator
hetero molecules

A: MarR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3884
Polymers33,8762
Non-polymers5132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area8710 Å2
ΔGint-50 kcal/mol
Surface area13270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.524, 65.524, 90.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-393-

HOH

21A-441-

HOH

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Components

#1: Protein MarR family transcriptional regulator


Mass: 16937.818 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: complex with palmitic acid / Source: (gene. exp.) Paenisporosarcina sp. TG-14 (bacteria) / Gene: E2636_00495 / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.86 Å3/Da / Density % sol: 57.02 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.6M ammonium citrate tribasic

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 26268 / % possible obs: 98 % / Redundancy: 26.4 % / Biso Wilson estimate: 23.63 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 82.4
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.422 / Num. unique obs: 1300

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Processing

Software
NameVersionClassification
REFMAC1.14_3260refinement
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→32.34 Å / SU ML: 0.1657 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.1222 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2547 1285 4.9 %
Rwork0.225 24918 -
obs0.2265 26203 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.78 Å2
Refinement stepCycle: LAST / Resolution: 1.6→32.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1100 0 18 143 1261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171127
X-RAY DIFFRACTIONf_angle_d1.87111504
X-RAY DIFFRACTIONf_chiral_restr0.1061180
X-RAY DIFFRACTIONf_plane_restr0.0142182
X-RAY DIFFRACTIONf_dihedral_angle_d24.8523450
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.660.26941330.23212750X-RAY DIFFRACTION99.69
1.66-1.740.25581480.21972762X-RAY DIFFRACTION100
1.74-1.830.24941460.2182784X-RAY DIFFRACTION100
1.83-1.940.24841400.22072785X-RAY DIFFRACTION100
1.94-2.090.26051420.2132804X-RAY DIFFRACTION100
2.09-2.30.251620.20432792X-RAY DIFFRACTION100
2.3-2.640.26061430.22022847X-RAY DIFFRACTION99.93
2.64-3.320.22511310.22472847X-RAY DIFFRACTION98.77
3.32-32.340.27271400.24062547X-RAY DIFFRACTION84.39

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