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- PDB-3ehh: Crystal structure of DesKC-H188V in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 3ehh
TitleCrystal structure of DesKC-H188V in complex with ADP
ComponentsSensor kinase (YocF protein)
KeywordsTRANSFERASE / four-helix bundle / GHL ATPase domain / Kinase
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
ADENOSINE-5'-DIPHOSPHATE / Sensor histidine kinase DesK
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 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

Downloads & links

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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)51,5166
Polymers50,5822
Non-polymers9354
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-67 kcal/mol
Surface area19960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.743, 124.050, 138.303
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A177 - 241
2114B177 - 241
1124A242 - 367
2124B242 - 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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*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


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.97 Å3/Da / Density % sol: 58.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG3350, CaCl2, 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: ID23-1 / Wavelength: 0.9793, 0.9795, 0.9756
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 31, 2007 / Details: Silicon toroidal mirror coated with Rhodium
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97951
30.97561
ReflectionRedundancy: 19.8 % / Av σ(I) over netI: 4.96 / Number: 222698 / Rmerge(I) obs: 0.07 / Rsym value: 0.106 / D res high: 2.2 Å / Num. obs: 57283 / % possible obs: 97.7
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)Rmerge(I) obsRsym valueRedundancy
1041.3548376.30.0310.08316.2
610222998.70.0330.07920.4
562061990.0360.07221.4
45472898.60.0390.08221.5
341311798.30.0580.10721.9
2.83518397.50.1240.14422.1
2.62.8695097.60.1760.19622.3
2.52.6435199.90.240.28222.4
2.42.5504395.70.3180.31315.7
2.32.4600098.80.4410.37314.5
2.22.3713896.90.585
ReflectionResolution: 2.097→41.345 Å / Num. all: 35284 / Num. obs: 35284 / % possible obs: 97.8 % / Redundancy: 19.8 % / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 4.961
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.1-2.2114.50.3731.87285150070.37396.5
2.21-2.3515.70.31327481347680.31397.1
2.35-2.5122.40.2822.410057244950.28297.6
2.51-2.7122.30.1963.49386842170.19698
2.71-2.9722.10.1444.58667239140.14498.4
2.97-3.3221.90.10767854035790.10798.7
3.32-3.8321.50.0828.26857231840.08298.5
3.83-4.721.40.0729.25783827010.07298.8
4.7-6.6420.40.07984441021780.07999
6.64-41.3516.20.0836.22008712410.08395.7

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Phasing

PhasingMethod: MAD
Phasing MAD set
IDR cullis acentricR cullis centricHighest resolution (Å)Lowest resolution (Å)Reflection acentricReflection centric
ISO_1002.619.98157922526
ISO_20.8370.8712.619.98157782514
ISO_30.86402.619.98156040
ANO_10.46402.619.98157460
ANO_20.45102.619.98157230
ANO_30.48502.619.98156040
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricReflection acentricReflection centric
ISO_110.11-19.980012294
ISO_17.66-10.1100310124
ISO_16.41-7.6600396132
ISO_15.63-6.4100484135
ISO_15.07-5.6300560137
ISO_14.66-5.0700626133
ISO_14.33-4.6600656132
ISO_14.06-4.3300750142
ISO_13.84-4.0600756121
ISO_13.65-3.8400842129
ISO_13.48-3.6500841122
ISO_13.34-3.4800910121
ISO_13.21-3.3400916112
ISO_13.1-3.2100965111
ISO_12.99-3.1001055133
ISO_12.9-2.99001052115
ISO_12.82-2.9001082125
ISO_12.74-2.82001138140
ISO_12.67-2.74001151124
ISO_12.6-2.67001180144
ANO_110.11-19.980.22501150
ANO_17.66-10.110.20403090
ANO_16.41-7.660.18503960
ANO_15.63-6.410.16604810
ANO_15.07-5.630.205600
ANO_14.66-5.070.25706240
ANO_14.33-4.660.27406560
ANO_14.06-4.330.31307450
ANO_13.84-4.060.34207550
ANO_13.65-3.840.38708380
ANO_13.48-3.650.4208400
ANO_13.34-3.480.46609060
ANO_13.21-3.340.52609160
ANO_13.1-3.210.59609610
ANO_12.99-3.10.685010530
ANO_12.9-2.990.735010520
ANO_12.82-2.90.767010770
ANO_12.74-2.820.814011380
ANO_12.67-2.740.875011510
ANO_12.6-2.670.869011730
ISO_210.11-19.980.8140.84611686
ISO_27.66-10.110.8370.855307124
ISO_26.41-7.660.8750.94395131
ISO_25.63-6.410.9330.955482134
ISO_25.07-5.630.9480.934560136
ISO_24.66-5.070.9210.922626133
ISO_24.33-4.660.8990.93656132
ISO_24.06-4.330.8950.931750142
ISO_23.84-4.060.90.903756121
ISO_23.65-3.840.9030.931842129
ISO_23.48-3.650.9090.93841122
ISO_23.34-3.480.8990.904909121
ISO_23.21-3.340.8890.908916112
ISO_23.1-3.210.8640.903965111
ISO_22.99-3.10.7930.8651055132
ISO_22.9-2.990.750.8631052115
ISO_22.82-2.90.7480.7541082125
ISO_22.74-2.820.6840.6811138140
ISO_22.67-2.740.6610.7041151124
ISO_22.6-2.670.6090.6211179144
ANO_210.11-19.980.39701020
ANO_27.66-10.110.32303040
ANO_26.41-7.660.28303950
ANO_25.63-6.410.26304820
ANO_25.07-5.630.29205560
ANO_24.66-5.070.34306240
ANO_24.33-4.660.35206560
ANO_24.06-4.330.37707480
ANO_23.84-4.060.37107560
ANO_23.65-3.840.43108400
ANO_23.48-3.650.4208380
ANO_23.34-3.480.42709050
ANO_23.21-3.340.46609150
ANO_23.1-3.210.50409620
ANO_22.99-3.10.584010550
ANO_22.9-2.990.605010520
ANO_22.82-2.90.659010740
ANO_22.74-2.820.695011350
ANO_22.67-2.740.767011500
ANO_22.6-2.670.793011740
ISO_310.11-19.980.860570
ISO_37.66-10.110.87802610
ISO_36.41-7.660.93603860
ISO_35.63-6.410.92604820
ISO_35.07-5.630.93405570
ISO_34.66-5.070.92406220
ISO_34.33-4.660.90906520
ISO_34.06-4.330.91807480
ISO_33.84-4.060.92207550
ISO_33.65-3.840.9108330
ISO_33.48-3.650.91608410
ISO_33.34-3.480.909040
ISO_33.21-3.340.89709130
ISO_33.1-3.210.85109610
ISO_32.99-3.10.811010510
ISO_32.9-2.990.789010510
ISO_32.82-2.90.789010740
ISO_32.74-2.820.733011370
ISO_32.67-2.740.716011500
ISO_32.6-2.670.683011690
ANO_310.11-19.980.3360570
ANO_37.66-10.110.29602610
ANO_36.41-7.660.31903860
ANO_35.63-6.410.3104820
ANO_35.07-5.630.32405570
ANO_34.66-5.070.43406220
ANO_34.33-4.660.41206520
ANO_34.06-4.330.44907480
ANO_33.84-4.060.45807550
ANO_33.65-3.840.46808330
ANO_33.48-3.650.48408410
ANO_33.34-3.480.50109040
ANO_33.21-3.340.53509130
ANO_33.1-3.210.57709610
ANO_32.99-3.10.647010510
ANO_32.9-2.990.652010510
ANO_32.82-2.90.699010740
ANO_32.74-2.820.739011370
ANO_32.67-2.740.799011500
ANO_32.6-2.670.811011690
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 21134
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.78-10075.10.733503
7.01-8.7869.70.776504
6.15-7.0171.40.788503
5.57-6.1567.50.798506
5.15-5.5759.70.826521
4.82-5.1561.10.852559
4.54-4.82600.877607
4.3-4.5456.70.87591
4.1-4.360.60.875675
3.93-4.157.20.874686
3.77-3.9360.80.875691
3.63-3.7758.40.873746
3.51-3.6359.50.861752
3.4-3.5159.20.864763
3.3-3.458.50.858830
3.2-3.363.90.847823
3.12-3.2630.858828
3.04-3.1265.70.839885
2.96-3.0464.50.85889
2.89-2.96650.842901
2.83-2.89670.83912
2.77-2.8371.70.835971
2.72-2.77680.807978
2.66-2.72710.839956
2.61-2.6672.60.834959
2.57-2.6168.30.7941060
2.5-2.5773.30.7361535

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
SHARPphasing
DM6phasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.099 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.156 / 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
Rfree0.232 1756 5 %RANDOM
Rwork0.193 33403 --
obs0.195 35159 97.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 192.21 Å2 / Biso mean: 47.06 Å2 / Biso min: 6.28 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å20 Å2
2--2.86 Å20 Å2
3----2.24 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 56 103 3180
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223171
X-RAY DIFFRACTIONr_bond_other_d0.0010.022183
X-RAY DIFFRACTIONr_angle_refined_deg1.7432.0064258
X-RAY DIFFRACTIONr_angle_other_deg0.97335371
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0425395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.32225.255137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.18515647
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0211523
X-RAY DIFFRACTIONr_chiral_restr0.0980.2496
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023412
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02565
X-RAY DIFFRACTIONr_mcbond_it1.0691.5979
X-RAY DIFFRACTIONr_mcbond_other0.2321.5402
X-RAY DIFFRACTIONr_mcangle_it1.7821575
X-RAY DIFFRACTIONr_scbond_it2.8113582
X-RAY DIFFRACTIONr_scangle_it4.8154.5520
Refine LS restraints NCS

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

Ens-IDNumberTypeRms dev position (Å)Weight position
1883MEDIUM POSITIONAL0.310.5
1883MEDIUM THERMAL1.542
21554MEDIUM POSITIONAL0.250.5
21554MEDIUM THERMAL1.862
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 124 -
Rwork0.224 2372 -
all-2496 -
obs--94.87 %
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)
12.22960.53481.16455.8095-0.78064.10410.0084-0.0145-0.2861-0.040.12110.02470.46060.0688-0.12950.08260.01920.00190.20560.04920.048916.81945.9846.887
27.50980.4171-0.97581.6417-3.641810.4314-0.06110.3461-0.17240.0270.07120.10470.4873-0.3138-0.010.1281-0.03450.05610.22460.05960.0642.56958.63225.486
34.17280.6263.05551.54061.673310.44330.08090.1929-0.1339-0.09810.0921-0.03910.0790.0401-0.1730.0117-0.0043-0.0020.1029-0.01440.005932.00154.16670.22
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A174 - 241
2X-RAY DIFFRACTION1B174 - 241
3X-RAY DIFFRACTION2A242 - 367
4X-RAY DIFFRACTION3B242 - 367

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