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- PDB-6chy: STRUCTURE OF CHEMOTAXIS PROTEIN CHEY -

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Basic information

Entry
Database: PDB / ID: 6chy
TitleSTRUCTURE OF CHEMOTAXIS PROTEIN CHEY
ComponentsCHEY
KeywordsSIGNAL TRANSDUCTION PROTEIN / 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 / bacterial-type flagellum / regulation of chemotaxis / thermotaxis / internal peptidyl-lysine acetylation / 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 / bacterial-type flagellum / regulation of chemotaxis / thermotaxis / internal peptidyl-lysine acetylation / 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 K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsZhu, X. / Rebello, J. / Matsumura, P. / Volz, K.
Citation
Journal: J.Biol.Chem. / Year: 1997
Title: Crystal structures of CheY mutants Y106W and T87I/Y106W. CheY activation correlates with movement of residue 106.
Authors: Zhu, X. / Rebello, J. / Matsumura, P. / Volz, K.
#1: Journal: J.Bacteriol. / Year: 1996
Title: Tyrosine 106 Plays an Important Role in Chemotaxis Signal Transduction in Escherichia Coli
Authors: Zhu, X. / Amsler, C.D. / Volz, K. / Matsumura, P.
#2: 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.
#3: Journal: Biochemistry / Year: 1993
Title: Structural Conservation in the Chey Superfamily
Authors: Volz, K.
#4: Journal: J.Biol.Chem. / Year: 1991
Title: Crystal Structure of Escherichia Coli Chey Refined at 1.7-A Resolution
Authors: Volz, K. / Matsumura, P.
History
DepositionAug 29, 1996Processing site: BNL
Revision 1.0Dec 7, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / 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_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: CHEY
B: CHEY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1293
Polymers28,0322
Non-polymers961
Water3,189177
1
A: CHEY


Theoretical massNumber of molelcules
Total (without water)14,0161
Polymers14,0161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CHEY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1122
Polymers14,0161
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: CHEY
hetero molecules

B: CHEY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2254
Polymers28,0322
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area1490 Å2
ΔGint-45 kcal/mol
Surface area11590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.780, 76.700, 32.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-210-

HOH

21A-211-

HOH

31A-212-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.78822, -0.61539, 0.00058), (-0.6152, 0.78795, -0.02562), (0.01531, -0.02055, -0.99967)
Vector: 76.9536, 26.924, 36.8423)

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Components

#1: Protein CHEY


Mass: 14016.225 Da / Num. of mol.: 2 / Mutation: T87I, Y106W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Plasmid: CHEY / Production host: Escherichia coli (E. coli) / References: UniProt: P06143, UniProt: P0AE67*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.14 Å3/Da / Density % sol: 42.47 %
Crystal growDetails: 18% PEG 3350 AND 0.2 M AMMONIUM SULFATE
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118 %PEG33501reservoir
20.2 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.033
DetectorDetector: CCD
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionHighest resolution: 2.3 Å / Num. obs: 7861 / % possible obs: 72.5 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.051
Reflection shellResolution: 2.33→2.45 Å / % possible all: 43.2
Reflection
*PLUS
% possible obs: 73 % / Num. measured all: 28137

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Processing

Software
NameClassification
MERLOTphasing
PROFFTrefinement
MADNESdata reduction
MADNESdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MODIFIED WILD-TYPE CHEY

Resolution: 2.33→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.185 --
obs-7698 72.5 %
Displacement parametersBiso mean: 11.04 Å2
Refinement stepCycle: LAST / Resolution: 2.33→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1951 0 5 177 2133
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_d0.0490.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.6051
X-RAY DIFFRACTIONp_mcangle_it1.0291.5
X-RAY DIFFRACTIONp_scbond_it0.5861
X-RAY DIFFRACTIONp_scangle_it0.9871.5
X-RAY DIFFRACTIONp_plane_restr0.0110.02
X-RAY DIFFRACTIONp_chiral_restr0.1630.15
X-RAY DIFFRACTIONp_singtor_nbd0.20.5
X-RAY DIFFRACTIONp_multtor_nbd0.2510.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2750.5
X-RAY DIFFRACTIONp_planar_tor23
X-RAY DIFFRACTIONp_staggered_tor20.915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor27.720
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.33 Å / Lowest resolution: 2.45 Å / Total num. of bins used: 7 / Num. reflection obs: 1474 / Rfactor obs: 0.222

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