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- PDB-6ep3: Lar controls the expression of the Listeria monocytogenes agr sys... -

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Basic information

Entry
Database: PDB / ID: 6ep3
TitleLar controls the expression of the Listeria monocytogenes agr system and mediates virulence.
ComponentsLmo0651 protein
KeywordsTRANSCRIPTION / Transcription factor / DNA binding protein / activator
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding
Similarity search - Function
GntR, C-terminal / FCD domain / Transcription regulator FadR/GntR, C-terminal / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsPinheiro, J. / Lisboa, J. / Carvalho, F. / Carreaux, A. / Santos, N. / Cabral, J. / Sousa, S. / Cabanes, D.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: MouR controls the expression of the Listeria monocytogenes Agr system and mediates virulence.
Authors: Pinheiro, J. / Lisboa, J. / Pombinho, R. / Carvalho, F. / Carreaux, A. / Brito, C. / Pontinen, A. / Korkeala, H. / Dos Santos, N.M.S. / Morais-Cabral, J.H. / Sousa, S. / Cabanes, D.
History
DepositionOct 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 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: Lmo0651 protein
B: Lmo0651 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,85419
Polymers52,2822
Non-polymers1,57117
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-69 kcal/mol
Surface area22600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.445, 122.445, 61.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Lmo0651 protein


Mass: 26141.119 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria)
Strain: ATCC BAA-679 / EGD-e / Gene: lmo0651 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y982
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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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: 4.38 Å3/Da / Density % sol: 71.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 1.5 M lithium sulfate, 100 mM sodium Hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980065, 0.97915
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9800651
20.979151
ReflectionResolution: 2.2→43.29 Å / Num. obs: 46113 / % possible obs: 99.3 % / Redundancy: 5.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1159 / Rpim(I) all: 0.05486 / Rsym value: 0.1285 / Net I/σ(I): 8.62
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 0.58 / Num. unique obs: 4603 / CC1/2: 0.444 / Rpim(I) all: 0.882 / % possible all: 96.92

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→43.29 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.67
RfactorNum. reflection% reflection
Rfree0.2485 2164 4.71 %
Rwork0.2201 --
obs0.2214 45954 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→43.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3558 0 89 85 3732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033700
X-RAY DIFFRACTIONf_angle_d0.5624971
X-RAY DIFFRACTIONf_dihedral_angle_d8.0892216
X-RAY DIFFRACTIONf_chiral_restr0.041537
X-RAY DIFFRACTIONf_plane_restr0.004622
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2004-2.25160.36381510.38452813X-RAY DIFFRACTION96
2.2516-2.30790.36831550.35912860X-RAY DIFFRACTION99
2.3079-2.37030.37861540.33252896X-RAY DIFFRACTION99
2.3703-2.440.35551380.32182941X-RAY DIFFRACTION100
2.44-2.51880.36181320.32352889X-RAY DIFFRACTION100
2.5188-2.60880.36681100.30492946X-RAY DIFFRACTION100
2.6088-2.71320.27411400.27282946X-RAY DIFFRACTION100
2.7132-2.83670.2441600.26092902X-RAY DIFFRACTION99
2.8367-2.98620.26481590.23972917X-RAY DIFFRACTION100
2.9862-3.17320.28181550.2542901X-RAY DIFFRACTION100
3.1732-3.41810.2541200.23172974X-RAY DIFFRACTION99
3.4181-3.76190.23121510.20432916X-RAY DIFFRACTION100
3.7619-4.30590.23651560.18942924X-RAY DIFFRACTION99
4.3059-5.42330.20491420.1732948X-RAY DIFFRACTION99
5.4233-43.29920.20811410.18563017X-RAY DIFFRACTION99
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)
10.6527-0.14880.10860.21140.30640.3623-0.0742-0.2515-0.032-0.08730.240.21090.3475-0.13470.0240.9282-0.12630.00690.44190.02280.7368-9.1883-53.4436.7306
20.4509-0.0539-0.01460.56090.21212.1494-0.03320.2208-0.0195-0.07080.08190.0373-0.03550.0123-00.49070.02760.02050.33480.00390.4147-2.8115-25.2857-3.4774
30.3037-0.11860.14230.4626-0.29620.21710.3172-0.193-0.2668-0.0465-0.2451-0.27410.32480.3532-0.00460.95950.12010.0170.49130.01350.836113.2131-53.932317.5317
40.08260.07040.05520.05050.0630.0428-0.18260.15130.0856-0.36010.65590.38480.37350.16830.00280.9828-0.0425-0.06470.42940.00110.75246.0911-51.056710.4048
5-0.04290.00240.02040.02040.03690.085-0.0663-0.03960.3334-0.490.1338-0.31450.37820.10470.01080.87970.04340.07710.57270.04090.666814.15-44.13576.2943
60.04490.18830.11590.61430.14830.5396-0.0473-0.13230.0701-0.04320.01080.0169-0.046-0.1446-00.54630.06880.01320.47220.01010.45041.6678-24.700825.037
70.0014-0.00810.0704-0.0038-0.05510.0576-0.3153-0.0246-0.04150.42110.24820.1846-0.0031-0.0587-00.66160.01930.00760.45530.01080.43693.3306-29.373727.0562
80.22760.3008-0.04140.4055-0.19040.55390.1037-0.4665-0.3354-0.131-0.00940.02780.5057-0.32870.00010.5648-0.0195-0.01530.3748-0.00190.49316.8272-33.21920.4193
90.2101-0.0098-0.1061-0.0399-0.08990.1995-0.1584-0.76710.65510.41890.0709-0.2507-0.55360.15870.01180.60650.01260.03370.413-0.11070.455.4491-17.537931.958
10-0.01370.0054-0.00420.0010.0886-0.0138-0.438-0.15120.2930.0850.4156-0.2851-0.15150.11860.00010.5765-0.03240.07750.4937-0.0610.573613.7322-19.304121.8959
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 76 )
2X-RAY DIFFRACTION2chain 'A' and (resid 77 through 217 )
3X-RAY DIFFRACTION3chain 'B' and (resid 3 through 43 )
4X-RAY DIFFRACTION4chain 'B' and (resid 44 through 63 )
5X-RAY DIFFRACTION5chain 'B' and (resid 64 through 76 )
6X-RAY DIFFRACTION6chain 'B' and (resid 77 through 125 )
7X-RAY DIFFRACTION7chain 'B' and (resid 126 through 144 )
8X-RAY DIFFRACTION8chain 'B' and (resid 145 through 172 )
9X-RAY DIFFRACTION9chain 'B' and (resid 173 through 194 )
10X-RAY DIFFRACTION10chain 'B' and (resid 195 through 220 )

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