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- PDB-3ehj: Crystal structure of DesKC-H188V in complex with AMP-PCP -

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Basic information

Entry
Database: PDB / ID: 3ehj
TitleCrystal structure of DesKC-H188V in complex with AMP-PCP
ComponentsSensor kinase (YocF protein)
KeywordsTRANSFERASE / four-helix bundle / GHL ATPase domain / Kinase
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / phosphoprotein phosphatase 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 / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsAlbanesi, D. / Alzari, P.M. / Buschiazzo, A.
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
DepositionSep 12, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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

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Assembly

Deposited unit
A: Sensor kinase (YocF protein)
B: Sensor kinase (YocF protein)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6726
Polymers50,5822
Non-polymers1,0914
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-59 kcal/mol
Surface area21700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.300, 34.300, 131.200
Angle α, β, γ (deg.)90.00, 96.60, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A180 - 242
2113B180 - 242
1123A245 - 367
2123B245 - 367

NCS ensembles :
ID
1
2

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Components

#1: Protein Sensor kinase (YocF protein) / DesK histidine kinase


Mass: 25290.947 Da / Num. of mol.: 2 / Fragment: entire cytoplasmic region / Mutation: H188V I183M I198M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yocF / Plasmid: pQE32 / Production host: Escherichia coli (E. coli) / 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.78 Å3/Da / Density % sol: 55.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG3350, CaCl2, bicine, ADP, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 16, 2007 / Details: toroidal focusing mirror
RadiationMonochromator: channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.5→19.8 Å / Num. obs: 19539 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 45.298 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 9.86
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 3.1 / % possible all: 96.8

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Processing

Software
NameVersionClassification
SHARPphasing
REFMAC5.5.0053refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→15 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 18.82 / SU ML: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.427 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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% reflectionSelection details
Rfree0.242 973 5 %RANDOM
Rwork0.198 18503 --
obs0.2 19476 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 131.42 Å2 / Biso mean: 49.916 Å2 / Biso min: 7.84 Å2
Baniso -1Baniso -2Baniso -3
1-1.49 Å20 Å2-0.94 Å2
2--0.51 Å20 Å2
3----2.21 Å2
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3268 0 64 53 3385
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223424
X-RAY DIFFRACTIONr_bond_other_d0.0020.022365
X-RAY DIFFRACTIONr_angle_refined_deg2.032.0014599
X-RAY DIFFRACTIONr_angle_other_deg1.06935799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3275422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.63225.096157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.10115693
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7451527
X-RAY DIFFRACTIONr_chiral_restr0.1020.2528
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023691
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02622
X-RAY DIFFRACTIONr_mcbond_it1.2041.52083
X-RAY DIFFRACTIONr_mcbond_other0.2451.5846
X-RAY DIFFRACTIONr_mcangle_it2.08123337
X-RAY DIFFRACTIONr_scbond_it3.09231341
X-RAY DIFFRACTIONr_scangle_it5.3234.51258
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1369TIGHT POSITIONAL0.070.05
1469LOOSE POSITIONAL0.075
1369TIGHT THERMAL0.240.5
1469LOOSE THERMAL0.6210
2698TIGHT POSITIONAL0.040.05
2828LOOSE POSITIONAL0.075
2698TIGHT THERMAL0.420.5
2828LOOSE THERMAL0.6710
LS refinement shellResolution: 2.5→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 69 -
Rwork0.236 1313 -
all-1382 -
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)
15.18430.3426-1.48981.31920.02832.88830.1242-0.1446-0.15260.0407-0.04670.0774-0.07210.008-0.07740.14190.0229-0.0110.0579-0.00410.107120.411-0.53829.243
21.28460.37680.7673.9420.271610.0208-0.04390.1849-0.10040.24020.0148-0.25250.02720.26920.0290.25850.0024-0.00510.0302-0.01260.091425.61714.43851.538
34.1715-0.31584.9063.91240.1478.1878-0.12410.0890.1630.17910.047-0.2680.03070.3420.07720.02580.0137-0.00220.0254-0.01210.102310.438-14.5779.149
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A163 - 242
2X-RAY DIFFRACTION1B156 - 242
3X-RAY DIFFRACTION2A243 - 368
4X-RAY DIFFRACTION3B243 - 369

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