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- PDB-2flk: Crystal structure of CheY in complex with CheZ(200-214) solved fr... -

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Basic information

Entry
Database: PDB / ID: 2flk
TitleCrystal structure of CheY in complex with CheZ(200-214) solved from a F432 crystal grown in CAPS (pH 10.5)
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
Protein phosphatase CheZ / Chemotaxis protein CheY
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 6, 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: Derived calculations / 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 / pdbx_struct_special_symmetry / 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)16,3025
Polymers15,7632
Non-polymers5393
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Chemotaxis protein cheY
B: C-terminal 15-mer from Chemotaxis protein cheZ
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)391,242120
Polymers378,31448
Non-polymers12,92972
Water86548
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_554-x,y,-z-11
crystal symmetry operation4_544x,-y-1,-z-11
crystal symmetry operation17_554x,z,-y-11
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_544-x,-z-1,-y-11
crystal symmetry operation20_545x,-z-1,y1
crystal symmetry operation57_554y+1/2,z,x-1/21
crystal symmetry operation58_454-y-1/2,z,-x-1/21
crystal symmetry operation59_544y+1/2,-z-1,-x-1/21
crystal symmetry operation60_444-y-1/2,-z-1,x-1/21
crystal symmetry operation69_554z+1/2,y,-x-1/21
crystal symmetry operation70_544z+1/2,-y-1,x-1/21
crystal symmetry operation71_454-z-1/2,y,x-1/21
crystal symmetry operation72_444-z-1/2,-y-1,-x-1/21
crystal symmetry operation77_545z+1/2,x-1/2,y1
crystal symmetry operation78_544z+1/2,-x-1/2,-y-11
crystal symmetry operation79_445-z-1/2,-x-1/2,y1
crystal symmetry operation80_444-z-1/2,x-1/2,-y-11
crystal symmetry operation85_544y+1/2,x-1/2,-z-11
crystal symmetry operation86_444-y-1/2,-x-1/2,-z-11
crystal symmetry operation87_545y+1/2,-x-1/2,z1
crystal symmetry operation88_445-y-1/2,x-1/2,z1
Buried area78490 Å2
ΔGint-786 kcal/mol
Surface area139780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)198.750, 198.750, 198.750
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-207-

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: 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
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID / CAPS (buffer)


Mass: 221.317 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 10.5
Details: 2M ammonium sulfate, 0.2M lithium sulfate, 0.1M CAPS, pH 10.5, 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
ReflectionResolution: 2.1→20 Å / Num. all: 20212 / Num. obs: 20143 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 27.3 Å2 / Rsym value: 0.1 / Net I/σ(I): 21.3
Reflection shellResolution: 2.1→2.17 Å / Mean I/σ(I) obs: 6.3 / Num. unique all: 1931 / Rsym value: 0.358 / % possible all: 98.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FQW

1fqw


Resolution: 2.1→19.96 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.965 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20736 1687 8.6 %RANDOM
Rwork0.19665 ---
all0.198 18410 --
obs0.19765 17947 97.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.041 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1084 0 33 80 1197
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221137
X-RAY DIFFRACTIONr_bond_other_d0.0010.021064
X-RAY DIFFRACTIONr_angle_refined_deg1.1842.0091527
X-RAY DIFFRACTIONr_angle_other_deg1.43432491
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.2583140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59815216
X-RAY DIFFRACTIONr_chiral_restr0.0630.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021229
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02202
X-RAY DIFFRACTIONr_nbd_refined0.2360.3233
X-RAY DIFFRACTIONr_nbd_other0.1920.31010
X-RAY DIFFRACTIONr_nbtor_other0.1170.51
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.578
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1250.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.36
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2150.336
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.58
X-RAY DIFFRACTIONr_mcbond_it0.7441.5707
X-RAY DIFFRACTIONr_mcangle_it1.48721124
X-RAY DIFFRACTIONr_scbond_it2.413430
X-RAY DIFFRACTIONr_scangle_it4.0954.5403
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 138 -
Rwork0.217 1340 -
obs-1478 98.7 %

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