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- PDB-4le1: Crystal structure of the receiver domain of DesR in the inactive state -

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Basic information

Entry
Database: PDB / ID: 4le1
TitleCrystal structure of the receiver domain of DesR in the inactive state
ComponentsTranscriptional regulatory protein DesR
KeywordsDNA BINDING PROTEIN / Response regulator / two-component system / transcription factor / receiver domain
Function / homology
Function and homology information


phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Winged helix-like DNA-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Transcriptional regulatory protein DesR
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.951 Å
AuthorsTrajtenberg, F. / Larrieux, N. / Buschiazzo, A.
CitationJournal: MBio / Year: 2014
Title: Allosteric activation of bacterial response regulators: the role of the cognate histidine kinase beyond phosphorylation.
Authors: Trajtenberg, F. / Albanesi, D. / Ruetalo, N. / Botti, H. / Mechaly, A.E. / Nieves, M. / Aguilar, P.S. / Cybulski, L. / Larrieux, N. / de Mendoza, D. / Buschiazzo, A.
History
DepositionJun 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulatory protein DesR
B: Transcriptional regulatory protein DesR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5566
Polymers30,2172
Non-polymers3394
Water2,306128
1
A: Transcriptional regulatory protein DesR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2933
Polymers15,1081
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcriptional regulatory protein DesR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2633
Polymers15,1081
Non-polymers1552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Transcriptional regulatory protein DesR
hetero molecules

A: Transcriptional regulatory protein DesR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5566
Polymers30,2172
Non-polymers3394
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+1/2,y+1/2,-z1
Buried area880 Å2
ΔGint-20 kcal/mol
Surface area13810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.732, 91.634, 62.106
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-128-

MET

21A-366-

HOH

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Components

#1: Protein Transcriptional regulatory protein DesR


Mass: 15108.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: desR, yocG, BSU19200 / Plasmid: pQE80L / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP10F' / References: UniProt: O34723
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.15 Å3/Da / Density % sol: 42.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.6 M (NH4)2SO4, 0.2 M NH4CH3CO2, vapor diffusion, hanging drop, temperature 291K, pH 8, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 9, 2011 / Details: mirrors
RadiationMonochromator: multilayer mirrors (Varimax-HF) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.951→62.106 Å / Num. all: 19564 / Num. obs: 19564 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rsym value: 0.058 / Net I/σ(I): 16.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.95-2.063.40.4341.8946927760.43498.3
2.06-2.183.50.2652.9934926850.265100
2.18-2.333.50.1764.4870124980.176100
2.33-2.523.50.1375.7834923590.137100
2.52-2.763.50.0978769921820.097100
2.76-3.093.50.06511.9697419730.065100
3.09-3.563.60.03721.2619817410.03799.9
3.56-4.363.50.02429.9527814980.02499.7
4.36-6.173.50.0234.8414611760.0299.2
6.17-36.873.40.01730.822826760.01797.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
XDSdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.951→19.99 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.9214 / Occupancy max: 1 / Occupancy min: 0.32 / SU R Cruickshank DPI: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2175 1000 5.12 %RANDOM
Rwork0.1919 ---
all0.1932 19523 --
obs0.1932 19523 99.25 %-
Displacement parametersBiso max: 101.15 Å2 / Biso mean: 30.4806 Å2 / Biso min: 9.31 Å2
Baniso -1Baniso -2Baniso -3
1-1.6918 Å20 Å20 Å2
2--0.877 Å20 Å2
3----2.5688 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.951→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 21 128 2101
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d755SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes53HARMONIC2
X-RAY DIFFRACTIONt_gen_planes304HARMONIC5
X-RAY DIFFRACTIONt_it2103HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion283SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2634SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2103HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg2835HARMONIC21.05
X-RAY DIFFRACTIONt_omega_torsion2.82
X-RAY DIFFRACTIONt_other_torsion16.46
LS refinement shellResolution: 1.95→2.06 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2395 148 5.4 %
Rwork0.2019 2592 -
all0.2037 2740 -
obs--99.25 %
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)
13.47450.0804-0.16031.81120.43271.41070.01630.07570.0267-0.0211-0.06170.035-0.13450.0750.0454-0.0317-0.0206-0.0098-0.0368-0.0006-0.06119.67168.08868.879
22.33331.24911.46613.62550.70593.4790.0045-0.0429-0.085-0.07260.0446-0.12040.38790.0085-0.04910.0281-0.00530.0132-0.02130.0077-0.063521.630432.821520.1816
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 132
2X-RAY DIFFRACTION2{ B|* }B1 - 130

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