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

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Basic information

Entry
Database: PDB / ID: 5iuj
TitleCrystal structure of the DesK-DesR complex in the phosphotransfer state with low Mg2+ (20 mM)
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)132,23916
Polymers130,0436
Non-polymers2,19610
Water27015
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)66,1208
Polymers65,0223
Non-polymers1,0985
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8950 Å2
ΔGint-69 kcal/mol
Surface area29510 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)66,1208
Polymers65,0223
Non-polymers1,0985
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8860 Å2
ΔGint-71 kcal/mol
Surface area29730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.820, 114.619, 91.597
Angle α, β, γ (deg.)90.000, 116.440, 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, 25 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.: 4 / 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.: 15 / 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: 3.17 Å3/Da / Density % sol: 61.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG3350, tri-potassium citrate, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 18, 2015 / Details: Kirkpatrick-Baez pair of bi-morph mirrors
RadiationMonochromator: channel cut cryogenically cooled monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 3.196→66.698 Å / Num. obs: 26369 / % possible obs: 97.4 % / Redundancy: 2.4 % / Biso Wilson estimate: 91.44 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 7.7
Reflection shellResolution: 3.196→3.207 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.731 / Mean I/σ(I) obs: 1.8 / % possible all: 96.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSJun 17, 2015data scaling
Aimless0.5.12data scaling
PHASER2.5.7phasing
BUSTER-TNT2.10.2refinement
Coot0.8.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→66.698 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.879 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.436
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1320 5.03 %RANDOM
Rwork0.187 ---
obs0.189 26231 97.3 %-
Displacement parametersBiso max: 212.94 Å2 / Biso mean: 93.13 Å2 / Biso min: 31.77 Å2
Baniso -1Baniso -2Baniso -3
1--4.2718 Å20 Å212.7425 Å2
2---16.5035 Å20 Å2
3---20.7753 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: final / Resolution: 3.2→66.698 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8869 0 130 15 9014
Biso mean--117.67 54.54 -
Num. residues----1118
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3504SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes292HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1298HARMONIC5
X-RAY DIFFRACTIONt_it9082HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1210SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance24HARMONIC1
X-RAY DIFFRACTIONt_utility_angle24HARMONIC1
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10298SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d9082HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg12209HARMONIC21.26
X-RAY DIFFRACTIONt_omega_torsion3.33
X-RAY DIFFRACTIONt_other_torsion20.83
LS refinement shellResolution: 3.2→3.33 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.278 157 5.27 %
Rwork0.24 2822 -
all-2979 -
obs--98.48 %
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)
10.7944-0.13440.25340.6351-0.88957.71080.0191-0.07940.01350.03110.05990.0318-0.02440.2345-0.079-0.1843-0.0648-0.0234-0.06680.0925-0.0574-12.5033.86872.689
25.8205-1.43212.81146.48230.38617.008-0.0901-0.24320.56130.49010.13150.1533-0.2487-0.7288-0.0414-0.2909-0.0052-0.00740.03580.1648-0.2679-39.68711.45853.431
35.0842-2.51914.02027.9378-0.57415.2135-0.06030.41040.38770.088-0.3935-0.0269-0.14340.39120.4538-0.1671-0.2038-0.13250.11460.0684-0.324211.54622.69861.526
43.58430.16931.82690.6149-0.11161.70550.0626-0.1655-0.03490.1432-0.0867-0.1348-0.09450.03810.0241-0.1824-0.08060.00240.0710.0139-0.1268-63.0437.138105.76
53.9739-1.22181.74095.36750.88798.63870.18360.4575-0.3089-0.13820.0549-0.03130.37820.3023-0.2385-0.1989-0.0199-0.08170.029-0.0613-0.276-66.231-0.79572.838
64.0679-1.4792-0.30548.31541.09996.89140.25540.0276-0.5045-0.0892-0.31360.30320.3038-0.30420.0582-0.1747-0.0704-0.14470.09540.1347-0.2447-83.921-12.26120.352
77.08932.03820.05216.7520.49176.3731-0.1071-0.0885-0.6265-0.17380.05620.12410.4433-0.56360.0509-0.1484-0.105-0.0019-0.26420.0327-0.0977-31.419-9.65387.103
85.10911.4256-0.51817.51720.06396.4704-0.1026-0.02740.3779-0.45070.3586-0.316-0.5090.5859-0.2561-0.0754-0.17690.1477-0.220.0145-0.1904-40.42519.21596.097
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|155 - A|242 B|154 - B|242 }A155 - 242
2X-RAY DIFFRACTION1{ A|155 - A|242 B|154 - B|242 }B154 - 242
3X-RAY DIFFRACTION2{ A|245 - A|367 A|401 - A|402 }A245 - 367
4X-RAY DIFFRACTION2{ A|245 - A|367 A|401 - A|402 }A401 - 402
5X-RAY DIFFRACTION3{ B|245 - B|368 B|401 - B|402 }B245 - 368
6X-RAY DIFFRACTION3{ B|245 - B|368 B|401 - B|402 }B401 - 402
7X-RAY DIFFRACTION4{ E|155 - E|242 D|154 - D|242 }E155 - 242
8X-RAY DIFFRACTION4{ E|155 - E|242 D|154 - D|242 }D154 - 242
9X-RAY DIFFRACTION5{ E|245 - E|501 }E245 - 501
10X-RAY DIFFRACTION6{ D|245 - D|368 D|401 - D|402 }D245 - 368
11X-RAY DIFFRACTION6{ D|245 - D|368 D|401 - D|402 }D401 - 402
12X-RAY DIFFRACTION7{ C|1 - C|131 }C1 - 131
13X-RAY DIFFRACTION8{ F|1 - F|131 }F1 - 131

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