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- PDB-1ffs: CHEY-BINDING DOMAIN OF CHEA IN COMPLEX WITH CHEY FROM CRYSTALS SO... -

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Basic information

Entry
Database: PDB / ID: 1ffs
TitleCHEY-BINDING DOMAIN OF CHEA IN COMPLEX WITH CHEY FROM CRYSTALS SOAKED IN ACETYL PHOSPHATE
Components
  • CHEMOTAXIS PROTEIN CHEA
  • CHEMOTAXIS PROTEIN CHEY
KeywordsTRANSFERASE/SIGNALING PROTEIN / doubly wound (beta/alpha)5 fold / TRANSFERASE-SIGNALING PROTEIN COMPLEX
Function / homology
Function and homology information


negative regulation of protein modification process / methyl accepting chemotaxis protein complex / positive regulation of post-translational protein modification / 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 / protein histidine kinase activity / internal peptidyl-lysine acetylation ...negative regulation of protein modification process / methyl accepting chemotaxis protein complex / positive regulation of post-translational protein modification / 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 / protein histidine kinase activity / internal peptidyl-lysine acetylation / thermotaxis / regulation of chemotaxis / bacterial-type flagellum / phosphorelay response regulator activity / protein acetylation / acetyltransferase activity / phosphorelay sensor kinase activity / histidine kinase / phosphorelay signal transduction system / establishment of localization in cell / chemotaxis / magnesium ion binding / signal transduction / ATP binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
CheY-binding domain of CheA / CheY binding / CheY binding / Histidine kinase CheA-like, homodimeric domain / CheY-binding domain of CheA / Histidine kinase CheA-like, homodimeric domain superfamily / Signal transducing histidine kinase, homodimeric domain / Signal transducing histidine kinase, homodimeric domain / : / CheW-like domain profile. ...CheY-binding domain of CheA / CheY binding / CheY binding / Histidine kinase CheA-like, homodimeric domain / CheY-binding domain of CheA / Histidine kinase CheA-like, homodimeric domain superfamily / Signal transducing histidine kinase, homodimeric domain / Signal transducing histidine kinase, homodimeric domain / : / CheW-like domain profile. / CheW-like domain / CheW-like domain superfamily / CheW-like domain / Two component signalling adaptor domain / Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / : / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Chemotaxis protein CheY / Chemotaxis protein CheA / Chemotaxis protein CheY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsGouet, P. / Chinardet, N. / Welch, M. / Guillet, V. / Birck, C. / Mourey, L. / Samama, J.-P.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Further insights into the mechanism of function of the response regulator CheY from crystallographic studies of the CheY--CheA(124--257) complex.
Authors: Gouet, P. / Chinardet, N. / Welch, M. / Guillet, V. / Cabantous, S. / Birck, C. / Mourey, L. / Samama, J.P.
#1: Journal: Nat.Struct.Biol. / Year: 1998
Title: Structure of the CheY-binding domain of histidine kinase CheA in complex with CheY.
Authors: WELCH, M. / CHINARDET, N. / MOUREY, L. / BIRCK, C. / SAMAMA, J.-P.
History
DepositionJul 26, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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_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: CHEMOTAXIS PROTEIN CHEY
B: CHEMOTAXIS PROTEIN CHEA
C: CHEMOTAXIS PROTEIN CHEY
D: CHEMOTAXIS PROTEIN CHEA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0316
Polymers56,9214
Non-polymers1102
Water4,306239
1
A: CHEMOTAXIS PROTEIN CHEY
B: CHEMOTAXIS PROTEIN CHEA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5153
Polymers28,4602
Non-polymers551
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: CHEMOTAXIS PROTEIN CHEY
D: CHEMOTAXIS PROTEIN CHEA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5153
Polymers28,4602
Non-polymers551
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)159.300, 53.400, 77.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CHEMOTAXIS PROTEIN CHEY


Mass: 13981.136 Da / Num. of mol.: 2 / Fragment: RESIDUES 124-257
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cellular location: CYTOPLASM / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli)
References: UniProt: P06143, UniProt: P0AE67*PLUS, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor
#2: Protein CHEMOTAXIS PROTEIN CHEA


Mass: 14479.338 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cellular location: CYTOPLASM / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: P07363
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.91 Å3/Da / Density % sol: 57.67 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% PEG MME 5K, 0.1 M MALONIC ACID, 0.1 M MES BUFFER 0.02 M DTT, 0.01 M MANGANESE CHLORIDE , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal grow
*PLUS
Details: Welch, M., (1998) Nature Struct. Biol., 5, 25.

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Oct 14, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 63874 / Num. obs: 26184 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Biso Wilson estimate: 48 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 11
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.2 / % possible all: 98
Reflection
*PLUS
Num. measured all: 63874
Reflection shell
*PLUS
% possible obs: 98.1 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.2

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.4→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.255 1772 RANDOM
Rwork0.217 --
all0.219 25738 -
obs0.219 25738 -
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2982 0 2 239 3223
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_torsion_deg23.8
X-RAY DIFFRACTIONc_torsion_impr_deg1.6
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 15 Å / σ(F): 0 / Rfactor obs: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.5

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