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- PDB-5lwl: MaeR D54A mutant response regulator bound to sulfate -

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Basic information

Entry
Database: PDB / ID: 5lwl
TitleMaeR D54A mutant response regulator bound to sulfate
ComponentsTranscriptional regulatory protein
KeywordsTRANSCRIPTION / Response regulator Beryllium trifluoride Catalytic aspartic acid
Function / homology
Function and homology information


phosphorelay response regulator activity / DNA binding / cytoplasm
Similarity search - Function
: / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily
Similarity search - Domain/homology
: / Transcriptional regulatory protein
Similarity search - Component
Biological speciesLactobacillus paracasei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsMiguel-Romero, L. / Casino, P. / Landete, J.M. / Monedero, V. / Zuniga, M. / Marina, A.
Funding support Spain, 3items
OrganizationGrant numberCountry
Spanish ministry of science and innovationAGL2007-60975 Spain
Spanish ministry of science and innovationAGL2010-15679 Spain
Generalitat ValencianaACOMP2012/137 Spain
CitationJournal: Sci Rep / Year: 2017
Title: The malate sensing two-component system MaeKR is a non-canonical class of sensory complex for C4-dicarboxylates.
Authors: Miguel-Romero, L. / Casino, P. / Landete, J.M. / Monedero, V. / Zuniga, M. / Marina, A.
History
DepositionSep 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Transcriptional regulatory protein
B: Transcriptional regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0404
Polymers27,8482
Non-polymers1922
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-71 kcal/mol
Surface area12620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.638, 76.638, 149.261
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Transcriptional regulatory protein


Mass: 13924.093 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus paracasei (bacteria) / Gene: LPL9_2999 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0K1MY03, UniProt: A0A247D6V9*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.93 Å3/Da / Density % sol: 68.67 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 1M lithium sulfate 0.5M ammonium sulfate 0.1M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97627 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97627 Å / Relative weight: 1
ReflectionResolution: 3.1→68.176 Å / Num. all: 7772 / Num. obs: 7772 / % possible obs: 99.2 % / Redundancy: 3.1 % / Rpim(I) all: 0.041 / Rrim(I) all: 0.074 / Rsym value: 0.061 / Net I/av σ(I): 9.5 / Net I/σ(I): 11.2 / Num. measured all: 23722
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
3.1-3.2730.541.4336711190.3730.6590.542.299.1
3.27-3.473.10.2952.6337110780.1970.3560.2953.699
3.47-3.713.10.1754.330759980.1190.2120.1755.699.6
3.71-42.90.116.627749470.0750.1330.117.699.5
4-4.383.10.0689.427198660.0460.0830.06811.399.5
4.38-4.93.10.04712.624147820.0310.0560.04715.799.3
4.9-5.6630.05113.620816910.0340.0620.05116.799.2
5.66-6.933.10.04714.617935850.0310.0560.04717.999.7
6.93-9.830.02822.413734560.0180.0340.02830.198.9
9.8-41.73130.02324.17552500.0150.0280.0234296.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
SCALA3.3.20data scaling
PDB_EXTRACT3.2data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LWK

5lwk


Resolution: 3.1→68.18 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.924 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.478 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2851 605 7.8 %RANDOM
Rwork0.2253 ---
obs0.2297 7157 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 190.17 Å2 / Biso mean: 116.774 Å2 / Biso min: 49.09 Å2
Baniso -1Baniso -2Baniso -3
1-8.52 Å2-0 Å2-0 Å2
2--8.52 Å2-0 Å2
3----17.05 Å2
Refinement stepCycle: final / Resolution: 3.1→68.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1958 0 10 8 1976
Biso mean--94.04 76.71 -
Num. residues----244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191990
X-RAY DIFFRACTIONr_angle_refined_deg1.2911.9762690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0115242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.8042490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.40215376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2471516
X-RAY DIFFRACTIONr_chiral_restr0.0790.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021422
X-RAY DIFFRACTIONr_mcbond_it2.58511.614973
X-RAY DIFFRACTIONr_mcangle_it4.57717.4111212
X-RAY DIFFRACTIONr_scbond_it2.3211.7481016
LS refinement shellResolution: 3.1→3.181 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.598 40 -
Rwork0.487 536 -
all-576 -
obs--98.46 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: -0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
1-30.519323.8391.6019
2-34.543717.52620.7179
3-33.621527.10371.2848
4-25.79732.30946.8859
5-11.943718.80119.4525
6-5.575419.697836.0956
7-4.441912.626737.4586
8-1.248521.510136.1318
9-6.42928.961530.2091
10000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 13
2X-RAY DIFFRACTION2A14 - 22
3X-RAY DIFFRACTION3A23 - 40
4X-RAY DIFFRACTION4A41 - 72
5X-RAY DIFFRACTION5A73 - 121
6X-RAY DIFFRACTION6B1 - 13
7X-RAY DIFFRACTION7B14 - 22
8X-RAY DIFFRACTION8B23 - 40
9X-RAY DIFFRACTION9B41 - 72
10X-RAY DIFFRACTION10B0

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