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- PDB-2fmi: Crystal structure of CheY in complex with CheZ 200-214 solved fro... -

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Basic information

Entry
Database: PDB / ID: 2fmi
TitleCrystal structure of CheY in complex with CheZ 200-214 solved from a F432 crystal grown in Tris (pH 8.4)
Components
  • C-terminal 15-mer from Chemotaxis protein cheZ
  • Chemotaxis protein cheY
KeywordsSIGNALING PROTEIN / CHEMOTAXIS / BEF(3)(-)-BOUND CHEY / CHEY-CHEZ PEPTIDE COMPLEX
Function / homology
Function and homology information


archaeal or bacterial-type flagellum-dependent cell motility / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / regulation of chemotaxis / bacterial-type flagellum / phosphorelay signal transduction system / phosphoprotein phosphatase activity / chemotaxis / metal ion binding / cytoplasm
Similarity search - Function
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 ...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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein phosphatase CheZ / Chemotaxis protein CheY
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.302 Å
AuthorsGuhaniyogi, J. / Robinson, V.L. / Stock, A.M.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structures of Beryllium Fluoride-free and Beryllium Fluoride-bound CheY in Complex with the Conserved C-terminal Peptide of CheZ Reveal Dual Binding Modes Specific to CheY Conformation.
Authors: Guhaniyogi, J. / Robinson, V.L. / Stock, A.M.
History
DepositionJan 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: Chemotaxis protein cheY
B: C-terminal 15-mer from Chemotaxis protein cheZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0735
Polymers15,7632
Non-polymers3103
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-12 kcal/mol
Surface area7640 Å2
MethodPISA
2
A: Chemotaxis protein cheY
B: C-terminal 15-mer from Chemotaxis protein cheZ
hetero molecules

A: Chemotaxis protein cheY
B: C-terminal 15-mer from Chemotaxis protein cheZ
hetero molecules

A: Chemotaxis protein cheY
B: C-terminal 15-mer from Chemotaxis protein cheZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,22015
Polymers47,2896
Non-polymers9319
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation57_554y+1/2,z,x-1/21
crystal symmetry operation77_545z+1/2,x-1/2,y1
Buried area6780 Å2
ΔGint-81 kcal/mol
Surface area18850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)198.280, 198.280, 198.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-150-

SO4

21A-150-

SO4

31A-151-

TRS

41A-151-

TRS

51A-232-

HOH

61A-233-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Chemotaxis protein cheY


Mass: 14140.385 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: cheY / Plasmid: pUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: P0A2D5
#2: Protein/peptide C-terminal 15-mer from Chemotaxis protein cheZ


Mass: 1622.687 Da / Num. of mol.: 1 / Fragment: residues 200-214 / Source method: obtained synthetically
Details: This sequence corresponds to the C-terminal 15 residues of the CheZ protein occurring naturally in Salmonella enterica serovar Typhumurium
References: UniProt: P07800

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Non-polymers , 4 types, 90 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 2M ammonium sulfate, 0.2M lithium sulfate, 0.1M Tris, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 16, 2003
RadiationMonochromator: KOHZU double crystal monochromator with a sagittally focused second crystal. Crystal type Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionNumber: 17416 / Rmerge(I) obs: 0.097 / Χ2: 1.086 / D res high: 2.2 Å / D res low: 20 Å / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
4.722097.910.0530.97
3.764.7299.610.061.051
3.283.7610010.0741.039
2.983.2810010.0971.058
2.772.9810010.1331.079
2.612.7799.910.1651.073
2.482.6110010.211.095
2.372.4899.910.2531.128
2.282.3710010.2641.113
2.22.2810010.3311.263
ReflectionResolution: 2.2→20 Å / Num. all: 17510 / Num. obs: 17416 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 34.5 Å2 / Rsym value: 0.097 / Χ2: 1.086 / Net I/σ(I): 22.8
Reflection shellResolution: 2.2→2.28 Å / Mean I/σ(I) obs: 8 / Num. unique all: 1695 / Rsym value: 0.331 / Χ2: 1.263 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FQW

1fqw


Resolution: 2.302→19.84 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.694 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21948 1518 10.1 %RANDOM
Rwork0.19283 ---
all0.19551 15290 --
obs0.19551 14963 97.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.285 Å2
Refinement stepCycle: LAST / Resolution: 2.302→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1090 0 19 87 1196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221128
X-RAY DIFFRACTIONr_angle_refined_deg1.2171.9981516
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9315140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.38426.27551
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34315208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.533154
X-RAY DIFFRACTIONr_chiral_restr0.080.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02825
X-RAY DIFFRACTIONr_nbd_refined0.1960.2495
X-RAY DIFFRACTIONr_nbtor_refined0.30.2774
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.274
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.210
X-RAY DIFFRACTIONr_mcbond_it0.8781.5740
X-RAY DIFFRACTIONr_mcangle_it1.35221127
X-RAY DIFFRACTIONr_scbond_it2.5333442
X-RAY DIFFRACTIONr_scangle_it4.1584.5389
LS refinement shellResolution: 2.302→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 99 -
Rwork0.198 955 -
obs-1054 95.73 %

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