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- PDB-1vlz: UNCOUPLED PHOSPHORYLATION AND ACTIVATION IN BACTERIAL CHEMOTAXIS:... -

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Basic information

Entry
Database: PDB / ID: 1vlz
TitleUNCOUPLED PHOSPHORYLATION AND ACTIVATION IN BACTERIAL CHEMOTAXIS: THE 2.1 ANGSTROM STRUCTURE OF A THREONINE TO ISOLEUCINE MUTANT AT POSITION 87 OF CHEY
ComponentsCHEY
KeywordsSIGNAL TRANSDUCTION PROTEIN / CHEY / RESPONSE REGULATORS / TWO-COMPONENT SYSTEMS
Function / homology
Function and homology information


bacterial-type flagellum basal body, C ring / bacterial-type flagellum rotor complex / bacterial-type flagellum-dependent swimming motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / internal peptidyl-lysine acetylation / thermotaxis / regulation of chemotaxis / bacterial-type flagellum / phosphorelay response regulator activity ...bacterial-type flagellum basal body, C ring / bacterial-type flagellum rotor complex / bacterial-type flagellum-dependent swimming motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / internal peptidyl-lysine acetylation / thermotaxis / regulation of chemotaxis / bacterial-type flagellum / phosphorelay response regulator activity / protein acetylation / acetyltransferase activity / phosphorelay signal transduction system / chemotaxis / magnesium ion binding / signal transduction / cytosol / 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 / Chemotaxis protein CheY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.05 Å
AuthorsGanguli, S. / Wang, H. / Matsumura, P. / Volz, K.
Citation
Journal: J.Biol.Chem. / Year: 1995
Title: Uncoupled phosphorylation and activation in bacterial chemotaxis. The 2.1-A structure of a threonine to isoleucine mutant at position 87 of CheY.
Authors: Ganguli, S. / Wang, H. / Matsumura, P. / Volz, K.
#1: Journal: Biochemistry / Year: 1993
Title: Structural Conservation in the Chey Superfamily
Authors: Volz, K.
#2: Journal: J.Biol.Chem. / Year: 1991
Title: Crystal Structure of Escherichia Coli Chey Refined at 1.7-Angstrom Resolution
Authors: Volz, K. / Matsumura, P.
History
DepositionApr 21, 1995Processing site: BNL
Revision 1.0Jul 10, 1995Provider: 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHEY
B: CHEY


Theoretical massNumber of molelcules
Total (without water)27,9862
Polymers27,9862
Non-polymers00
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.040, 72.470, 36.150
Angle α, β, γ (deg.)90.00, 109.06, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO A 110 / 2: CIS PROLINE - PRO B 110
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.04625, 0.26865, -0.96213), (0.09375, -0.96008, -0.26357), (-0.99452, -0.07801, -0.06959)
Vector: 43.19112, 25.73944, 64.56831)

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Components

#1: Protein CHEY


Mass: 13993.189 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: CHEY / References: UniProt: P06143, UniProt: P0AE67*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.39 Å3/Da / Density % sol: 48.54 %
Crystal grow
*PLUS
Temperature: 37 ℃ / Method: mid-log phase / Details: Matsumura, P., (1984) J. Bacteriol., 160, 36.

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Data collection

RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 15093 / % possible obs: 90.8 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.0457
Reflection
*PLUS
Highest resolution: 2.04 Å / Lowest resolution: 9999 Å / Num. measured all: 30935 / Rmerge(I) obs: 0.0457

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Processing

Software
NameClassification
PROFFTrefinement
XENGENdata reduction
RefinementResolution: 2.05→10 Å / σ(F): 2
Details: SOLVENT. MOST WATER MOLECULES ARE WELL BEHAVED. A FEW WATERS WITH HIGH TEMPERATURE FACTORS AND CLOSE CONTACTS WITH OTHER WATERS MAY BE PARTIAL SITES. SOLVENT MOLECULES HOH A 214 AND HOH B ...Details: SOLVENT. MOST WATER MOLECULES ARE WELL BEHAVED. A FEW WATERS WITH HIGH TEMPERATURE FACTORS AND CLOSE CONTACTS WITH OTHER WATERS MAY BE PARTIAL SITES. SOLVENT MOLECULES HOH A 214 AND HOH B 203 ARE PROBABLY AMMONIUM IONS.
RfactorNum. reflection
obs0.156 13198
Displacement parametersBiso mean: 16.3 Å2
Refinement stepCycle: LAST / Resolution: 2.05→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1898 0 0 172 2070
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0480.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.8571
X-RAY DIFFRACTIONp_mcangle_it1.5131.5
X-RAY DIFFRACTIONp_scbond_it1.0441
X-RAY DIFFRACTIONp_scangle_it1.81.5
X-RAY DIFFRACTIONp_plane_restr0.0110.02
X-RAY DIFFRACTIONp_chiral_restr0.1430.15
X-RAY DIFFRACTIONp_singtor_nbd0.1880.5
X-RAY DIFFRACTIONp_multtor_nbd0.1940.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2270.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.13
X-RAY DIFFRACTIONp_staggered_tor15.815
X-RAY DIFFRACTIONp_orthonormal_tor27.620
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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