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- PDB-2flw: Crystal structure of Mg2+ and BeF3- ound CheY in complex with Che... -

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Basic information

Entry
Database: PDB / ID: 2flw
TitleCrystal structure of Mg2+ and BeF3- ound CheY in complex with CheZ 200-214 solved from a F432 crystal grown in Hepes (pH 7.5)
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 / regulation of chemotaxis / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / 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 / Rossmann fold ...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
BERYLLIUM TRIFLUORIDE ION / Protein phosphatase CheZ / Chemotaxis protein CheY
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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: 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_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_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_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_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)15,9495
Polymers15,7632
Non-polymers1863
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)197.894, 197.894, 197.894
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-9048-

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, 92 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 7.5
Details: 2M ammonium sulfate, 0.2M lithium sulfate, 0.1M Hepes, pH 7.5, 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: 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: 2→30 Å / Num. all: 23007 / Num. obs: 22287 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 29.4 Å2 / Rsym value: 0.071 / Net I/σ(I): 35.5
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 8.2 / Num. unique all: 2197 / Rsym value: 0.261 / % possible all: 98.5

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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→30 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.288 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22767 2266 10.2 %RANDOM
Rwork0.21146 ---
all0.21311 20645 --
obs0.21311 20015 96.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.157 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1090 0 10 89 1189
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221157
X-RAY DIFFRACTIONr_angle_refined_deg1.2191.9861558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0045140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.82826.42956
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7215228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.514155
X-RAY DIFFRACTIONr_chiral_restr0.0860.2183
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02843
X-RAY DIFFRACTIONr_nbd_refined0.1960.2527
X-RAY DIFFRACTIONr_nbtor_refined0.2980.2800
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.285
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2740.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1010.213
X-RAY DIFFRACTIONr_mcbond_it0.7261.5748
X-RAY DIFFRACTIONr_mcangle_it1.21221151
X-RAY DIFFRACTIONr_scbond_it1.7073467
X-RAY DIFFRACTIONr_scangle_it2.7454.5407
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 143 -
Rwork0.22 1463 -
obs-1606 98.59 %

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