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- PDB-3gie: Crystal structure of DesKC_H188E in complex with AMP-PCP -

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Basic information

Entry
Database: PDB / ID: 3gie
TitleCrystal structure of DesKC_H188E in complex with AMP-PCP
ComponentsSensor histidine kinase desK
KeywordsTRANSFERASE / four-helix bundle / GHL ATPase domain / Cell membrane / Kinase / Membrane / Phosphoprotein / Transmembrane / Two-component regulatory system
Function / homology
Function and homology information


histidine kinase / phosphoprotein phosphatase activity / phosphorelay sensor kinase activity / protein dimerization activity / protein kinase activity / ATP binding / identical protein binding / plasma membrane
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 / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / 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 / Up-down Bundle ...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 / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / 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 / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Sensor histidine kinase DesK
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsTrajtenberg, F. / Albanesi, D. / Alzari, P.M. / Buschiazzo, A. / de Mendoza, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structural plasticity and catalysis regulation of a thermosensor histidine kinase
Authors: Albanesi, D. / Martin, M. / Trajtenberg, F. / Mansilla, M.C. / Haouz, A. / Alzari, P.M. / de Mendoza, D. / Buschiazzo, A.
History
DepositionMar 5, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 18, 2015Group: Refinement description
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / 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_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 / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: Sensor histidine kinase desK
B: Sensor histidine kinase desK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9726
Polymers49,9132
Non-polymers1,0594
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-54 kcal/mol
Surface area24290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.890, 94.050, 44.620
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2-

HOH

21B-3-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ARGARGGLYGLYchain A and (resseq 245:326 or resseq 336:366 )AA245 - 32693 - 174
121GLYGLYPROPROchain A and (resseq 245:326 or resseq 336:366 )AA336 - 366184 - 214
211ARGARGPROPROchain B and (resseq 245:366 )BB245 - 36693 - 214
112ILEILEVALVALchain A and (resseq 183:234 )AA183 - 23431 - 82
212ILEILEVALVALchain B and (resseq 183:234 )BB183 - 23431 - 82

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.999857, -0.016309, -0.004363), (-0.016219, -0.999669, 0.019956), (-0.004687, -0.019882, -0.999791)0.430376, 1.23527, 23.015301
2given(0.999663, -0.020196, 0.016336), (-0.019919, -0.999657, -0.016981), (0.016673, 0.01665, -0.999722)-0.295626, 1.69987, 22.1189

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Components

#1: Protein Sensor histidine kinase desK


Mass: 24956.590 Da / Num. of mol.: 2 / Fragment: entire cytoplasmic region / Mutation: H188E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yocF / Plasmid: pQE32 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)pLysS / References: UniProt: O34757, histidine kinase
#2: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.1 Å3/Da / Density % sol: 41.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: MPD, MgCl2, Hepes, AMP-PCP, pH 6, 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: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 17, 2008 / 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
Reflection twinOperator: -h,-k,l / Fraction: 0.528
ReflectionResolution: 2.65→27.165 Å / Num. all: 11757 / Num. obs: 11757 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.061
Reflection shellResolution: 2.65→2.75 Å / % possible all: 95.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX2009_02_15_2320_3refinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EHG and 3EHF

3ehg

3ehf


Resolution: 2.65→27.165 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 2 / Phase error: 28.99 / Stereochemistry target values: TWIN_LSQ_F
Details: Hydrogens have been added in the riding positions atom record contains sum of TLS and residual B anisou record contains sum of tls and residual U
RfactorNum. reflection% reflection
Rfree0.243 1097 9.33 %
Rwork0.194 10672 -
obs0.199 11757 97.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 81.214 Å2 / ksol: 0.285 e/Å3
Displacement parametersBiso max: 324.48 Å2 / Biso mean: 98.451 Å2 / Biso min: 19.67 Å2
Baniso -1Baniso -2Baniso -3
1--19.661 Å2-0 Å25.849 Å2
2---3.134 Å20 Å2
3----11.626 Å2
Refinement stepCycle: LAST / Resolution: 2.65→27.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3308 0 64 3 3375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083678
X-RAY DIFFRACTIONf_angle_d1.444566
X-RAY DIFFRACTIONf_chiral_restr0.085529
X-RAY DIFFRACTIONf_plane_restr0.004575
X-RAY DIFFRACTIONf_dihedral_angle_d22.5971347
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A895X-RAY DIFFRACTIONPOSITIONAL0.024
12B895X-RAY DIFFRACTIONPOSITIONAL0.024
21A408X-RAY DIFFRACTIONPOSITIONAL0.066
22B408X-RAY DIFFRACTIONPOSITIONAL0.066
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.651-2.7710.2931320.2721306143888
2.771-2.9170.3281200.2741323144389
2.917-3.0990.2951260.2481325145189
3.099-3.3380.31350.2381350148589
3.338-3.6730.2661450.2051329147489
3.673-4.2030.2181360.1831355149190
4.203-5.2880.2191420.1611340148289
5.288-25.670.2141400.1641344148487
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)
10.03720.02060.02450.09460.31940.27760.007-0.1219-0.132-0.0764-0.0275-0.1847-0.0739-0.1072-0.00080.1867-0.08150.00060.24290.07810.279722.65050.640411.1016
20.06510.0301-0.04150.0642-0.05160.0534-0.1333-0.0830.268-0.03490.1160.2055-0.1147-0.2665-00.58320.0642-0.25990.1468-0.17310.641838.8987-22.63955.6627
30.0596-0.02630.03640.0594-0.13820.1049-0.49850.1832-0.47830.0409-0.29880.086-0.037-0.0209-0.00150.7414-0.20490.34920.2662-0.34490.667338.505123.037617.8155
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 155:240) or (chain B and resseq 155:240)A155 - 240
2X-RAY DIFFRACTION1(chain A and resseq 155:240) or (chain B and resseq 155:240)B155 - 240
3X-RAY DIFFRACTION2chain A and resseq 245:366A245 - 366
4X-RAY DIFFRACTION3chain B and resseq 245:366B245 - 366

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