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- PDB-3gig: Crystal structure of phosphorylated DesKC in complex with AMP-PCP -

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Basic information

Entry
Database: PDB / ID: 3gig
TitleCrystal structure of phosphorylated DesKC in complex with AMP-PCP
Components(Sensor histidine kinase desK) x 2
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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Sensor histidine kinase DesK
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.502 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 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.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_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

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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)51,0696
Polymers50,0102
Non-polymers1,0594
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-60 kcal/mol
Surface area22700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.630, 94.630, 162.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
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
111ARGARGPHEPHEchain A and (resseq 245:331 or resseq 335:367 )AA245 - 33193 - 179
121HISHISASNASNchain A and (resseq 245:331 or resseq 335:367 )AA335 - 367183 - 215
211ARGARGASNASNchain B and (resseq 245:329 or resseq 332:367 )BB245 - 32993 - 177
221SERSERASNASNchain B and (resseq 245:329 or resseq 332:367 )BB332 - 367180 - 215
112GLNGLNSERSERchain A and (resseq 193:230 )AA193 - 23041 - 78
212GLNGLNSERSERchain B and (resseq 193:230 )BB193 - 23041 - 78

NCS ensembles :
ID
1
2

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Components

#1: Protein Sensor histidine kinase desK


Mass: 24965.623 Da / Num. of mol.: 1 / Fragment: entire cytoplasmic region
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: Protein Sensor histidine kinase desK


Mass: 25044.596 Da / Num. of mol.: 1 / Fragment: entire cytoplasmic region
Source method: isolated from a genetically manipulated source
Details: phosphorylated entire cytoplasmic region / 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
#3: 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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 4.2 Å3/Da / Density % sol: 70.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: PEG3000, MgCl2, CHES, AMP-PCP, pH 9.5, 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: Dec 9, 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
ReflectionResolution: 3.5→28.846 Å / Num. all: 11051 / Num. obs: 10993 / % possible obs: 99.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 92.42 Å2 / Rmerge(I) obs: 0.047
Reflection shellResolution: 3.5→3.6 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 4 / Num. measured obs: 3362 / Num. unique all: 864 / Num. unique obs: 864 / % possible all: 99.3

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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: 3.502→28.846 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: -0
Isotropic thermal model: two factors per residue (main chain + side chain), 5 body TLS model
Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 36.28 / Stereochemistry target values: ML
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
Rfree0.335 896 8.15 %random
Rwork0.287 10094 --
obs0.291 10990 99.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 79.815 Å2 / ksol: 0.245 e/Å3
Displacement parametersBiso max: 427.44 Å2 / Biso mean: 147.188 Å2 / Biso min: 33.98 Å2
Baniso -1Baniso -2Baniso -3
1--18.125 Å20 Å2-0 Å2
2---18.125 Å20 Å2
3----24.158 Å2
Refinement stepCycle: LAST / Resolution: 3.502→28.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2967 0 64 0 3031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0273337
X-RAY DIFFRACTIONf_angle_d2.7184178
X-RAY DIFFRACTIONf_chiral_restr0.167515
X-RAY DIFFRACTIONf_plane_restr0.012534
X-RAY DIFFRACTIONf_dihedral_angle_d25.661883
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A769X-RAY DIFFRACTIONPOSITIONAL0.235
12B769X-RAY DIFFRACTIONPOSITIONAL0.235
21A270X-RAY DIFFRACTIONPOSITIONAL0.116
22B270X-RAY DIFFRACTIONPOSITIONAL0.116
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.502-3.7210.3791390.36316461785100
3.721-4.0080.3811520.351635178799
4.008-4.410.3361490.3071654180399
4.41-5.0450.3471500.2621664181499
5.045-6.3450.3941560.32117081864100
6.345-28.8470.2741500.22617871937100
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)
1-0.0102-0.0071-0.01870.0045-0.0734-0.0601-0.3035-0.2565-0.3787-0.01610.16210.4399-0.6689-0.1853-00.8516-0.20060.0060.29380.02990.5502-35.297831.42693.7551
2-0.0093-0.014-0.00110.0065-0.00780.0108-0.9992-0.4293-0.44960.0941-0.24890.10070.4120.4643-00.432-1.5729-0.74-0.6855-0.58240.3879-29.220229.6293-5.7633
30.3553-0.17020.01020.2080.03310.0913-0.0005-0.11240.0569-0.2922-0.46010.3575-0.08380.084200.581-0.9930.0496-1.48970.29980.1738-17.02759.909-12.7867
40.0918-0.0882-0.0116-0.019-0.12050.1538-0.07060.1691-0.24620.14770.22790.1881-0.5160.2943-00.7754-0.2236-0.05530.4494-0.19810.8299-37.86220.8516-22.5483
50.09820.0838-0.14170.0607-0.14760.1046-0.0601-0.698-0.0507-0.39630.21640.56930.78080.4133-01.11590.0121-0.13740.5106-0.09730.3581.533736.096513.2488
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resseq 155:183A155 - 183
2X-RAY DIFFRACTION2chain B and resseq 165:183B165 - 183
3X-RAY DIFFRACTION3chain A, B and resseq 184:240A184 - 240
4X-RAY DIFFRACTION4chain A and resseq 243:367A243 - 367
5X-RAY DIFFRACTION5chain B and resseq 243:367B243 - 367

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