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- PDB-2che: STRUCTURE OF THE MG2+-BOUND FORM OF CHEY AND MECHANISM OF PHOSPHO... -

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Basic information

Entry
Database: PDB / ID: 2che
TitleSTRUCTURE OF THE MG2+-BOUND FORM OF CHEY AND MECHANISM OF PHOSPHORYL TRANSFER IN BACTERIAL CHEMOTAXIS
ComponentsCHEY
KeywordsSIGNAL TRANSDUCTION PROTEIN
Function / homology
Function and homology information


archaeal or bacterial-type flagellum-dependent cell motility / phosphorelay signal transduction system / chemotaxis / metal ion binding / cytoplasm
Similarity search - Function
: / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chemotaxis protein CheY
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsStock, A. / Martinez-Hackert, E. / Rasmussen, B. / West, A. / Stock, J. / Ringe, D. / Petsko, G.
Citation
Journal: Biochemistry / Year: 1993
Title: Structure of the Mg(2+)-bound form of CheY and mechanism of phosphoryl transfer in bacterial chemotaxis.
Authors: Stock, A.M. / Martinez-Hackert, E. / Rasmussen, B.F. / West, A.H. / Stock, J.B. / Ringe, D. / Petsko, G.A.
#1: Journal: J.Biol.Chem. / Year: 1991
Title: Roles of the Highly Conserved Aspartate and Lysine Residues in the Response Regulator of Bacterial Chemotaxis
Authors: Lukat, G.S. / Lee, B.H. / Mottonen, J.M. / Stock, A.M. / Stock, J.B.
#2: Journal: Biochemistry / Year: 1990
Title: Divalent Metal Ion Binding to the Chey Protein and its Significance to Phosphotransfer in Bacterial Chemotaxis
Authors: Lukat, G.S. / Stock, A.M. / Stock, J.B.
#3: Journal: Nature / Year: 1990
Title: Signal Transduction in Bacteria
Authors: Stock, J.B. / Stock, A.M. / Mottonen, J.M.
History
DepositionJan 17, 1994Processing site: BNL
Revision 1.0Apr 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_conn.ptnr2_label_seq_id / _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: CHEY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0332
Polymers14,0091
Non-polymers241
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.710, 46.980, 53.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO 110

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Components

#1: Protein CHEY


Mass: 14009.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / References: UniProt: P0A2D5
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.45 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 mMCheY protein1drop
250 mMsodium acetate1drop
31.9 Mammonium sulfate1drop
450 mMsodium acetate1drop
51-2 %PEG4001drop
61.9 Mammonium sulfate-sodium acetate solution1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 9999 Å / Num. obs: 10659 / % possible obs: 95 % / Num. measured all: 49659 / Rmerge(I) obs: 0.069

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementHighest resolution: 1.8 Å / σ(F): 0 /
RfactorNum. reflection
obs0.19 49659
Refinement stepCycle: LAST / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms981 0 1 96 1078
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.02
X-RAY DIFFRACTIONp_angle_d0.0410.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0440.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.9361
X-RAY DIFFRACTIONp_mcangle_it1.4991.5
X-RAY DIFFRACTIONp_scbond_it1.4691
X-RAY DIFFRACTIONp_scangle_it2.3841.5
X-RAY DIFFRACTIONp_plane_restr0.020.025
X-RAY DIFFRACTIONp_chiral_restr0.2260.15
X-RAY DIFFRACTIONp_singtor_nbd0.2110.5
X-RAY DIFFRACTIONp_multtor_nbd0.3050.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2930.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.35
X-RAY DIFFRACTIONp_staggered_tor2215
X-RAY DIFFRACTIONp_orthonormal_tor25.615
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Lowest resolution: 5 Å / Num. reflection obs: 49659 / Rfactor obs: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS

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