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- PDB-3gif: Crystal structure of DesKC_H188E in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 3gif
TitleCrystal structure of DesKC_H188E in complex with ADP
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


phosphorelay sensor kinase activity / histidine kinase / phosphoprotein phosphatase activity / protein kinase activity / protein dimerization activity / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1930 / : / DesK N-terminal domain / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1930 / : / DesK N-terminal domain / 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 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 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 1.2Nov 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.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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)50,3804
Polymers49,9132
Non-polymers4672
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-56 kcal/mol
Surface area15550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.580, 93.480, 59.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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 (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.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.55 Å3/Da / Density % sol: 51.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG3350, CaCl2, Tris, KCl, ADP, pH 7.5, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 28, 2009
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.7→36.27 Å / Num. all: 14581 / Num. obs: 14581 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 58.5 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.062
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2079 / Rsym value: 0.497 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3ehg

3ehf


Resolution: 2.7→36.27 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.06 / σ(F): 2 / Phase error: 32.04 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.317 726 5 %RANDOM
Rwork0.254 13780 --
obs0.257 14506 99.66 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.372 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso max: 108.34 Å2 / Biso mean: 63.139 Å2 / Biso min: 34.38 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.7→36.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2176 0 28 20 2224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182443
X-RAY DIFFRACTIONf_angle_d2.0012998
X-RAY DIFFRACTIONf_chiral_restr0.114364
X-RAY DIFFRACTIONf_plane_restr0.006383
X-RAY DIFFRACTIONf_dihedral_angle_d22.096840
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.9080.351420.28626912833100
2.908-3.2010.3571430.27127242867100
3.201-3.6640.3531440.25527352879100
3.664-4.6140.2571460.21627642910100
4.614-36.2730.311510.2642866301799

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