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- PDB-1fqw: CRYSTAL STRUCTURE OF ACTIVATED CHEY -

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Basic information

Entry
Database: PDB / ID: 1fqw
TitleCRYSTAL STRUCTURE OF ACTIVATED CHEY
ComponentsCHEMOTAXIS CHEY PROTEIN
KeywordsSIGNALING PROTEIN / response regulator / Activated CheY / Chemotaxis / two-component signal transduction / BeF3 / receiver domain
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 / cytoplasm / cytosol
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
BERYLLIUM TRIFLUORIDE ION / : / Chemotaxis protein CheY / Chemotaxis protein CheY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.37 Å
AuthorsLee, S.Y. / Cho, H.S. / Pelton, J.G. / Yan, D. / Berry, E.A. / Wemmer, D.E.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: Crystal structure of activated CheY. Comparison with other activated receiver domains.
Authors: Lee, S.Y. / Cho, H.S. / Pelton, J.G. / Yan, D. / Berry, E.A. / Wemmer, D.E.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: NMR structure of Activated CheY
Authors: Cho, H.S. / Lee, S.Y. / Yan, D. / Pan, X. / Parkinson, J.S. / Kustu, S. / Wemmer, D.E. / Pelton, J.G.
#2: Journal: J.Mol.Biol. / Year: 1999
Title: Phosphorylated Aspartate in the Structure of a Response Regulator Protein
Authors: Lewis, R.J. / Brannigan, J.A. / Muchova, K. / Barak, I. / Wilkinson, A.J.
#3: Journal: Structure / Year: 1999
Title: Conformational changes induced by phosphorylation of the FixJ receiver domain
Authors: Birck, C. / Mourey, L. / Gouet, P. / Fabry, B. / Schumacher, J. / Rousseau, P. / Kahn, D. / Samama, J.P.
#4: Journal: Biochemistry / Year: 2000
Title: The 1.9A resolution Crystal structure of Phosphono-CheY, an Analogue of the Active Form of the Response Regulator, CheY
Authors: Halkides, C.J. / McEvoy, M.M. / Casper, E. / Matsumura, P. / Volz, K. / Dahlquist, F.W.
History
DepositionSep 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 7, 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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_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: CHEMOTAXIS CHEY PROTEIN
B: CHEMOTAXIS CHEY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2046
Polymers27,9622
Non-polymers2424
Water3,117173
1
A: CHEMOTAXIS CHEY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1023
Polymers13,9811
Non-polymers1212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CHEMOTAXIS CHEY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1023
Polymers13,9811
Non-polymers1212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.684, 53.911, 161.532
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer from each chain.

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Components

#1: Protein CHEMOTAXIS CHEY PROTEIN


Mass: 13981.136 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid details: PET21 / Production host: Escherichia coli (E. coli) / References: UniProt: P06143, UniProt: P0AE67*PLUS
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 4.18 Å3/Da / Density % sol: 70.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Ammonium sulfate, Tris buffer, MnCl2, glycerol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 8.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12 mMprotein1drop
28 mM1dropBeCl2
350 mM1dropNaF
44 mM1dropMnCl2
51.8 Mammonium sulfate1reservoir
65-10 %glycerol1reservoir
7100 mMTris1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 17, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.37→25 Å / Num. all: 89177 / Num. obs: 17703 / % possible obs: 89.1 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 39.4 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 13.2
Reflection shellResolution: 2.37→2.41 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.23 / Num. unique all: 500 / % possible all: 52.2
Reflection
*PLUS
Num. measured all: 89177
Reflection shell
*PLUS
% possible obs: 52.2 % / Rmerge(I) obs: 0.23

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.37→15 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 643531.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 846 4.8 %RANDOM
Rwork0.21 ---
all0.211 17550 --
obs0.21 17594 89.7 %-
Displacement parametersBiso mean: 44.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.16 Å20 Å2
3----0.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.37→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1958 0 10 173 2141
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.751.5
X-RAY DIFFRACTIONc_mcangle_it5.062
X-RAY DIFFRACTIONc_scbond_it6.472
X-RAY DIFFRACTIONc_scangle_it8.162.5
Refine LS restraints NCSNCS model details: CONSTRAINED
LS refinement shellResolution: 2.37→2.52 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.317 122 4.5 %
Rwork0.282 2569 -
obs--83.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2PARAM19.RCV
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION4MN_PARAMMN_TOP
Software
*PLUS
Name: CNS / Version: 0.1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 4.8 % / Rfactor obs: 0.21 / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 44.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.93
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.317 / % reflection Rfree: 4.5 % / Rfactor Rwork: 0.282

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