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- PDB-3dge: Structure of a histidine kinase-response regulator complex reveal... -

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Basic information

Entry
Database: PDB / ID: 3dge
TitleStructure of a histidine kinase-response regulator complex reveals insights into Two-component signaling and a novel cis-autophosphorylation mechanism
Components
  • Response regulator
  • Sensor protein
KeywordsTRANSFERASE/SIGNALING PROTEIN / four-helix bundle / ATP binding domain / receiver domain / Kinase / Phosphoprotein / TRANSFERASE / TRANSFERASE-SIGNALING PROTEIN COMPLEX
Function / homology
Function and homology information


histidine phosphotransfer kinase activity / histidine kinase / phosphorelay sensor kinase activity / phosphorelay signal transduction system / nucleotide binding / identical protein binding / metal ion binding
Similarity search - Function
Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain ...Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Histidine kinase-like ATPase, C-terminal domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / Heat Shock Protein 90 / CheY-like superfamily / Response regulator / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / CITRIC ACID / Response regulator / histidine kinase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsCasino, P. / Marina, A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2009
Title: Structural Insight into Partner Specificity and Phosphoryl Transfer in Two-Component Signal Transduction.
Authors: Casino, P. / Rubio, V. / Marina, A.
History
DepositionJun 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sensor protein
C: Response regulator
B: Sensor protein
D: Response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6929
Polymers86,4534
Non-polymers1,2395
Water2,918162
1
A: Sensor protein
C: Response regulator
B: Sensor protein
D: Response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,5008
Polymers86,4534
Non-polymers1,0474
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10640 Å2
ΔGint-115 kcal/mol
Surface area31950 Å2
MethodPISA
2
B: Sensor protein
D: Response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7504
Polymers43,2272
Non-polymers5232
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-43 kcal/mol
Surface area18280 Å2
MethodPISA
3
A: Sensor protein
C: Response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7504
Polymers43,2272
Non-polymers5232
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-40 kcal/mol
Surface area18200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.958, 90.668, 68.985
Angle α, β, γ (deg.)90.000, 108.420, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-142-

HOH

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Sensor protein /


Mass: 29378.281 Da / Num. of mol.: 2 / Fragment: Cytoplasmic domain, UNP residues 232-481
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_0853 / Plasmid: pET24b / Production host: Escherichia coli (E. coli) / Strain (production host): RIL / References: UniProt: Q9WZV7, histidine kinase
#2: Protein Response regulator /


Mass: 13848.256 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_0468 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): RIL / References: UniProt: Q9WYT9

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Non-polymers , 4 types, 167 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63.31 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.7M ammonium sulfate, 2.5% dioxane, 0.1M citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM1610.97935, 0.97950, 0.95298
SYNCHROTRONESRF ID14-320.931
Detector
TypeIDDetectorDateDetails
MAR CCD 165 mm1CCDJan 1, 2004mirror
ADSC QUANTUM 42CCDJan 1, 2004Toroidal mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111), 140 x 80 x 20 mmMADMx-ray1
2Diamond (111), Ge(220)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979351
20.97951
30.952981
40.9311
ReflectionResolution: 2.8→43.64 Å / Num. all: 26588 / Num. obs: 116062 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 4.4 % / Biso Wilson estimate: 79 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 16.2
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.8 / Num. unique all: 3875 / Rsym value: 0.4 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.006data extraction
APEXdata collection
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementResolution: 2.8→43.64 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.912 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 32.729 / SU ML: 0.325 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.363 / ESU R Free: 0.393 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1326 5 %RANDOM
Rwork0.234 ---
all0.236 25230 --
obs0.236 116062 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 110.42 Å2 / Biso mean: 74.876 Å2 / Biso min: 20.52 Å2
Baniso -1Baniso -2Baniso -3
1--2.57 Å20 Å2-0.84 Å2
2--3.78 Å20 Å2
3----1.74 Å2
Refinement stepCycle: LAST / Resolution: 2.8→43.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5712 0 77 162 5951
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0225884
X-RAY DIFFRACTIONr_angle_refined_deg1.5562.0037961
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5085714
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.75125.154260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.017151114
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3811532
X-RAY DIFFRACTIONr_chiral_restr0.0950.2920
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024290
X-RAY DIFFRACTIONr_nbd_refined0.2580.23007
X-RAY DIFFRACTIONr_nbtor_refined0.3190.23943
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.2290
X-RAY DIFFRACTIONr_metal_ion_refined0.1840.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.270.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2190.25
X-RAY DIFFRACTIONr_mcbond_it1.2091.53680
X-RAY DIFFRACTIONr_mcangle_it1.54425810
X-RAY DIFFRACTIONr_scbond_it2.37332461
X-RAY DIFFRACTIONr_scangle_it3.4914.52151
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.428 96 -
Rwork0.377 1871 -
all-1967 -
obs--100 %
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)
11.46620.06990.42140.8465-0.35791.92880.13480.06910.0623-0.04050.08960.07050.0438-0.2615-0.2244-0.1001-0.0006-0.00110.08040.0411-0.070656.49162.72321.708
27.04722.234-1.21992.6363-0.21664.22970.3755-0.3159-0.18410.3567-0.3103-0.04170.5685-0.3433-0.0652-0.0677-0.33510.05750.08250.0066-0.14640.92844.6733.49
33.1055-1.52522.10142.3519-2.58195.82250.29910.43970.3568-0.2843-0.2737-0.1168-0.0852-0.0783-0.0254-0.02970.25160.03150.14480.2019-0.089150.95980.4612.771
44.5223-1.7705-1.57622.30820.69853.0172-0.2951-0.49770.28930.39970.3928-0.1196-0.3417-0.1002-0.0977-0.01810.1832-0.01690.1017-0.0594-0.119655.70777.51842.012
52.8191.86530.6633.00382.12025.1538-0.3720.8354-0.4536-0.29840.6547-0.3480.18020.4028-0.2827-0.1068-0.09440.04990.2421-0.2194-0.036568.1947.7235.028
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA245 - 31714 - 86
2X-RAY DIFFRACTION1BC245 - 31714 - 86
3X-RAY DIFFRACTION2AA324 - 48193 - 250
4X-RAY DIFFRACTION3BC324 - 48193 - 250
5X-RAY DIFFRACTION4CB1 - 1221 - 122
6X-RAY DIFFRACTION5DD1 - 1221 - 122

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