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- PDB-1kmi: CRYSTAL STRUCTURE OF AN E.COLI CHEMOTAXIS PROTEIN, CHEZ -

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Basic information

Entry
Database: PDB / ID: 1kmi
TitleCRYSTAL STRUCTURE OF AN E.COLI CHEMOTAXIS PROTEIN, CHEZ
Components
  • Chemotaxis protein cheY
  • Chemotaxis protein cheZ
KeywordsSIGNALING PROTEIN / four-helix bundle
Function / homology
Function and homology information


methyl accepting chemotaxis protein complex / bacterial-type flagellum basal body, C ring / bacterial-type flagellum rotor complex / bacterial-type flagellum-dependent swimming motility / archaeal or bacterial-type flagellum-dependent cell motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / bacterial-type flagellum / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / regulation of chemotaxis ...methyl accepting chemotaxis protein complex / bacterial-type flagellum basal body, C ring / bacterial-type flagellum rotor complex / bacterial-type flagellum-dependent swimming motility / archaeal or bacterial-type flagellum-dependent cell motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / bacterial-type flagellum / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / regulation of chemotaxis / thermotaxis / internal peptidyl-lysine acetylation / phosphorelay response regulator activity / protein acetylation / phosphoprotein phosphatase activity / acetyltransferase activity / phosphorelay signal transduction system / protein dephosphorylation / chemotaxis / magnesium ion binding / signal transduction / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Helix hairpin bin / Single helix bin / Chemotaxis phosphatase, CheZ / Chemotaxis phosphatase, CheZ / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator ...Helix hairpin bin / Single helix bin / Chemotaxis phosphatase, CheZ / Chemotaxis phosphatase, CheZ / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / Up-down Bundle / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BERYLLIUM TRIFLUORIDE ION / Chemotaxis protein CheY / Protein phosphatase CheZ / Chemotaxis protein CheY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsZhao, R. / Collins, E.J. / Bourret, R.B. / Silversmith, R.E.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Structure and catalytic mechanism of the E. coli chemotaxis phosphatase CheZ.
Authors: Zhao, R. / Collins, E.J. / Bourret, R.B. / Silversmith, R.E.
History
DepositionDec 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _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_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
Y: Chemotaxis protein cheY
Z: Chemotaxis protein cheZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3655
Polymers38,1112
Non-polymers2533
Water0
1
Y: Chemotaxis protein cheY
Z: Chemotaxis protein cheZ
hetero molecules

Y: Chemotaxis protein cheY
Z: Chemotaxis protein cheZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,73010
Polymers76,2234
Non-polymers5076
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area12360 Å2
ΔGint-109 kcal/mol
Surface area31500 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)163.280, 163.280, 54.133
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe biological (CheY/CheZ)2 dimer is made of two (CheY/CheZ) monomeric complexes which are related by a crystallographic two-fold symmetry.

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Components

#1: Protein Chemotaxis protein cheY / / CHEY


Mass: 14112.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K0642RECA-PRBB40 / References: UniProt: P06143, UniProt: P0AE67*PLUS
#2: Protein Chemotaxis protein cheZ / / CHEZ


Mass: 23999.037 Da / Num. of mol.: 1 / Mutation: E134K / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K0642RECA-PRBB40 / References: UniProt: P0A9H9
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#5: Chemical ChemComp-BCN / BICINE / Bicine


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.8 Å3/Da / Density % sol: 74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: isopropanol, ammonium acetate, bicine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.264 mMCheY1drop
23.6 mM1dropBeCl2
310 mM1dropNaF
410 mM1dropMgCl2
50.264 mMCheZ E134K1drop
60.1 MBicine1reservoirpH8.5
70.2 Mammonium acetate1reservoir
830 %(v/v)isopropanol1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12001
22001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2511.0087
SYNCHROTRONNSLS X4A20.9789,0.9786,0.9562,1.6490,1.6486,1.5853
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDAug 20, 2000mirror
BRANDEIS - B42CCDSep 21, 2000mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1KOHZU double crystal monochromatorSINGLE WAVELENGTHMx-ray1
2non-dispersive double crystal monochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.00871
20.97891
30.97861
40.95621
51.6491
61.64861
71.58531
ReflectionResolution: 2.9→30 Å / Num. all: 14532 / Num. obs: 14532 / % possible obs: 88 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 22.3
Reflection shellResolution: 2.9→3 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 3.1 / Num. unique all: 1449 / % possible all: 0.896
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 88 % / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 3 Å / % possible obs: 89.6 % / Rmerge(I) obs: 0.457

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Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD
Starting model: PDB ENTRY 1FQW AS A PARTIAL MODEL

1fqw


Resolution: 2.9→20 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.298 563 random
Rwork0.279 --
all-14532 -
obs-11330 -
Refine analyzeLuzzati coordinate error obs: 0.6 Å
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 16 0 2385
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.54
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_dihedral_angle_d20.245
Refinement
*PLUS
Lowest resolution: 20 Å / Num. reflection obs: 10767 / % reflection Rfree: 5 % / Rfactor Rfree: 0.298 / Rfactor Rwork: 0.279
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.54
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.245
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78

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