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- PDB-2fmk: Crystal structure of Mg2+ and BeF3- bound CheY in complex with Ch... -

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Basic information

Entry
Database: PDB / ID: 2fmk
TitleCrystal structure of Mg2+ and BeF3- bound CheY in complex with CheZ 200-214 solved from a P2(1)2(1)2 crystal grown in MES (pH 6.0)
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 / bacterial-type flagellum / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / regulation of chemotaxis / phosphoprotein phosphatase activity / phosphorelay signal transduction system / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chemotaxis protein CheY / BERYLLIUM TRIFLUORIDE ION / Protein phosphatase CheZ / Protein phosphatase CheZ
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.999 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

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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)15,8794
Polymers15,7892
Non-polymers902
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-13 kcal/mol
Surface area7280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.189, 61.953, 36.617
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-9077-

HOH

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Components

#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: 1648.725 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, UniProt: Q57N83*PLUS
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 1.95 Å3/Da / Density % sol: 36.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 37.5% PEG 8000, 0.05M sodium phosphate (monobasic), 0.1M MES, pH 6.0, 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: 1.0718 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 13, 2004
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: 1.0718 Å / Relative weight: 1
ReflectionResolution: 1.999→30 Å / Num. all: 8820 / Num. obs: 8762 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Rsym value: 0.052 / Net I/σ(I): 38.6
Reflection shellResolution: 1.999→2.07 Å / Mean I/σ(I) obs: 21.5 / Num. unique all: 845 / Rsym value: 0.08 / % possible all: 99.3

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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
Resolution: 1.999→30 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.894 / SU B: 4.062 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.246 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.232 871 10 %RANDOM
Rwork0.186 ---
all0.19064 8782 --
obs0.19064 8735 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.921 Å2
Baniso -1Baniso -2Baniso -3
1--1.22 Å20 Å20 Å2
2---0.09 Å20 Å2
3---1.31 Å2
Refinement stepCycle: LAST / Resolution: 1.999→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1098 0 5 90 1193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221131
X-RAY DIFFRACTIONr_angle_refined_deg1.1161.9831520
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.265141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.68426.53852
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5315215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.093154
X-RAY DIFFRACTIONr_chiral_restr0.0760.2177
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02830
X-RAY DIFFRACTIONr_nbd_refined0.1970.2541
X-RAY DIFFRACTIONr_nbtor_refined0.2980.2785
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.281
X-RAY DIFFRACTIONr_metal_ion_refined0.0140.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2740.219
X-RAY DIFFRACTIONr_mcbond_it0.5321.5744
X-RAY DIFFRACTIONr_mcangle_it0.90121140
X-RAY DIFFRACTIONr_scbond_it1.43435
X-RAY DIFFRACTIONr_scangle_it2.34.5380
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 73 -
Rwork0.196 560 -
obs-633 99.37 %

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