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- PDB-5iul: Crystal structure of the DesK-DesR complex in the phosphotransfer... -

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Basic information

Entry
Database: PDB / ID: 5iul
TitleCrystal structure of the DesK-DesR complex in the phosphotransfer state with high Mg2+ (150 mM) and BeF3
Components
  • Sensor histidine kinase DesK
  • Transcriptional regulatory protein DesR
KeywordsTRANSFERASE / Two-component regulatory system / Kinase / Response regulator / Phosphotransfer complex / Phosphotransfer
Function / homology
Function and homology information


histidine kinase / phosphorelay signal transduction system / phosphoprotein phosphatase activity / phosphorelay sensor kinase 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 / phosphoprotein phosphatase activity / phosphorelay sensor kinase 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
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 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. / CheY-like superfamily / Response regulator / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Winged helix-like DNA-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / 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 / FOURIER SYNTHESIS / Resolution: 3.153 Å
AuthorsTrajtenberg, F. / Imelio, J.A. / Larrieux, N. / Buschiazzo, A.
CitationJournal: Elife / Year: 2016
Title: Regulation of signaling directionality revealed by 3D snapshots of a kinase:regulator complex in action.
Authors: Trajtenberg, F. / Imelio, J.A. / Machado, M.R. / Larrieux, N. / Marti, M.A. / Obal, G. / Mechaly, A.E. / Buschiazzo, A.
History
DepositionMar 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Jan 4, 2017Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)132,28818
Polymers130,0436
Non-polymers2,24512
Water32418
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)66,18310
Polymers65,0223
Non-polymers1,1627
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8990 Å2
ΔGint-80 kcal/mol
Surface area29210 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)66,1058
Polymers65,0223
Non-polymers1,0835
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8990 Å2
ΔGint-81 kcal/mol
Surface area28970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.186, 116.680, 91.877
Angle α, β, γ (deg.)90.000, 117.100, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 6 molecules ABDECF

#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 / Plasmid: pACYC-Duet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O34757, histidine kinase
#2: Protein Transcriptional regulatory protein DesR


Mass: 15108.367 Da / Num. of mol.: 2 / Fragment: Receiver domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: desR, yocG, BSU19200 / Plasmid: pACYC-Duet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O34723

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Non-polymers , 4 types, 30 molecules

#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: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.24 Å3/Da / Density % sol: 61.99 % / Mosaicity: 0.23 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEGi3350, tri-potassium citrate, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 31, 2015 / 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: 3.153→38.59 Å / Num. obs: 28033 / % possible obs: 97.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 84.1 Å2 / CC1/2: 0.997 / Net I/σ(I): 11.8
Reflection shellResolution: 3.153→3.163 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.5 / % possible all: 67.4

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Processing

Software
NameVersionClassification
XDSJun 17, 2015data scaling
Aimless0.5.15data scaling
BUSTER-TNT2.10.2refinement
Coot0.8.2model building
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.153→38.59 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.879 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.396
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1361 4.86 %RANDOM
Rwork0.19 ---
obs0.192 28015 97.5 %-
Displacement parametersBiso max: 291.57 Å2 / Biso mean: 89.62 Å2 / Biso min: 35.02 Å2
Baniso -1Baniso -2Baniso -3
1-11.4072 Å20 Å23.5979 Å2
2---25.844 Å20 Å2
3---14.4368 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: final / Resolution: 3.153→38.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8709 0 132 18 8859
Biso mean--121.07 65.57 -
Num. residues----1102
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3430SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes288HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1273HARMONIC5
X-RAY DIFFRACTIONt_it8912HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1194SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance36HARMONIC1
X-RAY DIFFRACTIONt_utility_angle41HARMONIC1
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10167SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8912HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg11981HARMONIC21.25
X-RAY DIFFRACTIONt_omega_torsion3.42
X-RAY DIFFRACTIONt_other_torsion20.08
LS refinement shellResolution: 3.15→3.27 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.271 132 4.81 %
Rwork0.24 2615 -
all-2747 -
obs--92.1 %
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)
10.74810.03710.38670.5517-1.35117.3662-0.00550.12260.10450.0272-0.00410.1102-0.11470.13210.0096-0.0456-0.077-0.0787-0.02940.1313-0.1808-15.776614.7325-9.3735
25.7114-0.90871.75127.24970.52194.03710.0247-0.16950.61450.49150.04670.2277-0.4638-0.6981-0.0714-0.06610.0515-0.03030.09810.1971-0.3972-42.922221.9975-28.9856
36.2267-2.88792.52037.9856-0.74546.3641-0.1340.41040.3838-0.2752-0.2557-0.1922-0.1337-0.06790.3897-0.1599-0.2037-0.12960.05350.0644-0.34777.595934.6137-20.1424
45.84851.17763.15331.11260.622.62170.0081-0.3065-0.02470.1137-0.1311-0.10040.1184-0.28030.1229-0.0874-0.17340.00270.00670.0053-0.2666-66.522418.361923.2932
56.0279-0.87020.16686.5908-0.12116.408-0.1030.5021-0.4492-0.4443-0.0579-0.24880.42670.12750.1609-0.153-0.1083-0.06560.0379-0.1219-0.3804-69.607810.7936-9.6342
65.1384-0.93380.73968.29662.79158.65450.14650.1514-0.43910.1043-0.07830.23090.5067-0.3476-0.0682-0.1594-0.087-0.09990.01320.1262-0.3901-87.0171-1.385237.2654
75.72440.09490.34465.7713-0.51726.56070.0612-0.0272-0.45170.12480.0110.38830.6368-0.3319-0.0722-0.0741-0.06030.0163-0.26770.0043-0.1145-34.98911.30264.8794
85.62861.16490.90236.13130.53538.3916-0.03090.33010.4887-0.3510.0566-0.5088-0.56140.5219-0.0257-0.0089-0.06420.1515-0.28690.0613-0.0914-43.84830.356413.8747
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|155 - A|242 B|154 - B|243 }A155 - 242
2X-RAY DIFFRACTION1{ A|155 - A|242 B|154 - B|243 }B154 - 243
3X-RAY DIFFRACTION2{ A|1 A|245 - A|368 }A1
4X-RAY DIFFRACTION2{ A|1 A|245 - A|368 }A245 - 368
5X-RAY DIFFRACTION3{ B|1 B|245 - B|367 }B1
6X-RAY DIFFRACTION3{ B|1 B|245 - B|367 }B245 - 367
7X-RAY DIFFRACTION4{ E|155 - E|239 D|155 - D|242 }E155 - 239
8X-RAY DIFFRACTION4{ E|155 - E|239 D|155 - D|242 }D155 - 239
9X-RAY DIFFRACTION5{ E|1 E|245 - E|368 }E1
10X-RAY DIFFRACTION5{ E|1 E|245 - E|368 }E245 - 368
11X-RAY DIFFRACTION6{ D|1 D|245 - D|368 }D1
12X-RAY DIFFRACTION6{ D|1 D|245 - D|368 }D245 - 368
13X-RAY DIFFRACTION7{ C|1 - C|131 }C1 - 131
14X-RAY DIFFRACTION8{ F|1 - F|131 }F1 - 131

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