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- PDB-7ssi: CRYSTAL STRUCTURE OF THE DESK:DESR-Q10A COMPLEX IN THE PHOSPHOTRA... -

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Basic information

Entry
Database: PDB / ID: 7ssi
TitleCRYSTAL STRUCTURE OF THE DESK:DESR-Q10A COMPLEX IN THE PHOSPHOTRANSFER STATE
Components
  • Sensor histidine kinase DesK
  • Transcriptional regulatory protein DesR
KeywordsTRANSFERASE / TWO-COMPONENT REGULATORY SYSTEM / KINASE / RESPONSE REGULATOR / PHOSPHOTRANSFER COMPLEX / PHOSPHOTRANSFER / TRAN GENE REGULATION COMPLEX / TRANSFERASE-GENE REGULATION complex
Function / homology
Function and homology information


histidine kinase / phosphorelay signal transduction system / phosphorelay sensor kinase activity / phosphoprotein phosphatase activity / protein dimerization activity / protein kinase activity / regulation of DNA-templated transcription / DNA binding / ATP binding / identical protein binding ...histidine kinase / phosphorelay signal transduction system / phosphorelay sensor kinase activity / phosphoprotein phosphatase activity / protein dimerization activity / protein kinase activity / regulation of DNA-templated transcription / DNA binding / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1930 / Signal transduction histidine kinase, subgroup 3, dimerisation and phosphoacceptor domain / : / Histidine kinase / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1930 / Signal transduction histidine kinase, subgroup 3, dimerisation and phosphoacceptor domain / : / Histidine kinase / 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. / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / CheY-like superfamily / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Transcriptional regulatory protein DesR / Sensor histidine kinase DesK
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.41 Å
AuthorsTrajtenberg, F. / Buschiazzo, A.
Funding supportUruguay, 1items
OrganizationGrant numberCountry
Agencia Nacional de Investigacion e Innovacion (ANII)FCE_1_2017_1_136291Uruguay
CitationJournal: Sci.Signal. / Year: 2023
Title: An allosteric switch ensures efficient unidirectional information transmission by the histidine kinase DesK from Bacillus subtilis.
Authors: Lima, S. / Blanco, J. / Olivieri, F. / Imelio, J.A. / Nieves, M. / Carrion, F. / Alvarez, B. / Buschiazzo, A. / Marti, M.A. / Trajtenberg, F.
History
DepositionNov 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Sensor histidine kinase DesK
B: Sensor histidine kinase DesK
C: Transcriptional regulatory protein DesR
D: Sensor histidine kinase DesK
E: Sensor histidine kinase DesK
F: Transcriptional regulatory protein DesR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,09616
Polymers129,9296
Non-polymers2,16710
Water18010
1
A: Sensor histidine kinase DesK
B: Sensor histidine kinase DesK
C: Transcriptional regulatory protein DesR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0488
Polymers64,9643
Non-polymers1,0835
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8540 Å2
ΔGint-82 kcal/mol
Surface area28330 Å2
MethodPISA
2
D: Sensor histidine kinase DesK
E: Sensor histidine kinase DesK
F: Transcriptional regulatory protein DesR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0488
Polymers64,9643
Non-polymers1,0835
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8900 Å2
ΔGint-79 kcal/mol
Surface area28340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.067, 115.634, 91.374
Angle α, β, γ (deg.)90, 116.74, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Sensor histidine kinase DesK


Mass: 24956.590 Da / Num. of mol.: 4 / Fragment: Fragment: entire cytoplasmic region / Mutation: H188E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: desK, yocF, BSU19190 / Production host: Escherichia coli (E. coli) / References: UniProt: O34757, histidine kinase
#2: Protein Transcriptional regulatory protein DesR


Mass: 15051.316 Da / Num. of mol.: 2 / Mutation: Q10A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: desR, yocG, BSU19200 / Production host: Escherichia coli (E. coli) / References: UniProt: O34723
#3: Chemical
ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.2 Å3/Da / Density % sol: 61.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG3350, tri-potassium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 14, 2016 / Details: mirrors
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.41→34.41 Å / Num. obs: 22186 / % possible obs: 99.6 % / Redundancy: 3.6 % / Rrim(I) all: 0.172 / Net I/σ(I): 7.5
Reflection shellResolution: 3.41→3.46 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1046 / CC1/2: 0.446 / Rrim(I) all: 1.599 / % possible all: 93.8

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROC1.0.5 20200520data processing
Aimless0.7.4data scaling
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IUK

5iuk


Resolution: 3.41→34.41 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.902 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.586
RfactorNum. reflection% reflectionSelection details
Rfree0.2834 1085 -RANDOM
Rwork0.2518 ---
obs0.2534 22186 99 %-
Displacement parametersBiso mean: 122.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.6948 Å20 Å29.2502 Å2
2---16.4909 Å20 Å2
3---12.7961 Å2
Refine analyzeLuzzati coordinate error obs: 0.56 Å
Refinement stepCycle: LAST / Resolution: 3.41→34.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8668 0 130 10 8808
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0088872HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0511943HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3387SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1558HARMONIC5
X-RAY DIFFRACTIONt_it8872HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1202SEMIHARMONIC5
X-RAY DIFFRACTIONt_utility_distance20HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact7080SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.85
X-RAY DIFFRACTIONt_other_torsion20.08
LS refinement shellResolution: 3.41→3.44 Å
RfactorNum. reflection% reflection
Rfree0.4012 26 -
Rwork0.3695 --
obs0.3712 444 71.59 %
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)
10.43720.76031.99320.4455-2.137514.48640.11030.12030.22620.12030.19050.32510.22620.3251-0.3008-0.0850.1075-0.05120.20920.1295-0.1581-15.103713.2506-6.8324
27.07520.07291.3697.77320.35027.42920.23210.185-0.64750.1850.0797-0.9768-0.6475-0.9768-0.3118-0.14710.0126-0.05260.27120.199-0.2309-42.935721.5758-28.1927
39.1574-4.81771.19189.2990.56425.4838-0.12520.0295-0.41130.0295-0.33250.0724-0.41130.07240.4577-0.1306-0.3563-0.27990.39360.1537-0.44487.467633.9844-20.4573
49.99761.66936.03950.32320.55625.2014-0.14390.15890.02550.15890.0585-0.39580.0255-0.39580.0854-0.1552-0.0932-0.04770.1742-0.0361-0.1402-64.132219.750725.0737
55.8687-1.87561.72019.0349-0.10758.25690.0367-0.33530.8209-0.3353-0.20380.34080.82090.34080.1671-0.0955-0.1137-0.08290.3349-0.1166-0.3558-68.987710.9763-9.5921
65.1519-3.72360.854410.47864.43119.60990.51160.07480.73330.0748-0.4894-0.78750.7333-0.7875-0.0222-0.0793-0.2362-0.16770.3230.2967-0.4756-86.6043-0.863137.0942
79.3908-0.27051.16458.47581.27566.93920.1099-0.37310.7662-0.37310.1008-1.10950.7662-1.1095-0.2107-0.1036-0.1268-0.0988-0.24910.09220.0407-34.62741.45945.2418
86.19920.1118-0.23679.2242-1.271510.8099-0.1071-0.7359-0.7316-0.73590.02460.9554-0.73160.95540.08250.0627-0.11960.1491-0.1881-0.0566-0.2713-43.325730.338813.7806
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|155 - A|242 B|164 - B|242 }A155 - 242
2X-RAY DIFFRACTION1{ A|155 - A|242 B|164 - B|242 }B164 - 242
3X-RAY DIFFRACTION2{ A|245 - A|368 }A245 - 368
4X-RAY DIFFRACTION3{ B|245 - B|367 }B245 - 367
5X-RAY DIFFRACTION4{ D|155 - D|242 E|164 - E|242 }D155 - 242
6X-RAY DIFFRACTION4{ D|155 - D|242 E|164 - E|242 }E164 - 242
7X-RAY DIFFRACTION5{ D|245 - D|368 }D245 - 368
8X-RAY DIFFRACTION6{ E|245 - E|367 }E245 - 367
9X-RAY DIFFRACTION7{ C|0 - C|131 }C0 - 131
10X-RAY DIFFRACTION8{ F|0 - F|132 }F0 - 132

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