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- PDB-3olv: Structural and functional effects of substitution at position T+1... -

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Basic information

Entry
Database: PDB / ID: 3olv
TitleStructural and functional effects of substitution at position T+1 in CheY: CheYA88V-BeF3-Mg complex
ComponentsChemotaxis protein CheY
KeywordsSIGNALING PROTEIN / alpha-beta repeat / chemotaxis / two-component signaling / response regulator / CheA / CheZ / phosphorylation
Function / homology
Function and homology information


bacterial-type flagellum basal body, C ring / bacterial-type flagellum rotor complex / bacterial-type flagellum-dependent swimming motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / bacterial-type flagellum / regulation of chemotaxis / thermotaxis / internal peptidyl-lysine acetylation / phosphorelay response regulator activity ...bacterial-type flagellum basal body, C ring / bacterial-type flagellum rotor complex / bacterial-type flagellum-dependent swimming motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / bacterial-type flagellum / regulation of chemotaxis / thermotaxis / internal peptidyl-lysine acetylation / phosphorelay response regulator activity / acetyltransferase activity / phosphorelay signal transduction system / chemotaxis / magnesium ion binding / signal transduction / cytosol / cytoplasm
Similarity search - Function
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 / Chemotaxis protein CheY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.697 Å
AuthorsImmormino, R.M. / Bourret, R.B.
CitationJournal: Biochemistry / Year: 2016
Title: A Variable Active Site Residue Influences the Kinetics of Response Regulator Phosphorylation and Dephosphorylation.
Authors: Immormino, R.M. / Silversmith, R.E. / Bourret, R.B.
History
DepositionAug 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Oct 19, 2016Group: Database references
Revision 1.3Sep 6, 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_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_asym_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_asym_id / _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_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

Downloads & links

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Assembly

Deposited unit
A: Chemotaxis protein CheY
B: Chemotaxis protein CheY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,91812
Polymers28,2812
Non-polymers63710
Water5,963331
1
A: Chemotaxis protein CheY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5257
Polymers14,1401
Non-polymers3846
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chemotaxis protein CheY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3935
Polymers14,1401
Non-polymers2524
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.477, 44.799, 48.069
Angle α, β, γ (deg.)69.23, 68.01, 66.16
Int Tables number1
Space group name H-MP1
DetailsEach protomer constitutes a biological molecule

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Components

#1: Protein Chemotaxis protein CheY /


Mass: 14140.387 Da / Num. of mol.: 2 / Mutation: A88V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: cheY / Plasmid: pRS3 / Production host: Escherichia coli (E. coli) / Strain (production host): K0641 RecA / References: UniProt: P0AE67
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: BeF3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Ammonium Sulfate 1.7 M Glycerol 5% (v/v) Tris 100 mM pH 8.0 MnCl2 20mM BeCl2 1mM NaF 10mM, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 8, 2010 / Details: Sagital crystal
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 31472 / Num. obs: 29238 / % possible obs: 92.9 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 21.61 Å2 / Rsym value: 0.058 / Net I/σ(I): 25.3
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
1.7-1.7325.410800.174167
1.73-1.762.16.611270.167173.4
1.76-1.792.36.212850.204180.6
1.79-1.832.47.813140.181184.9
1.83-1.872.69.314600.166190.2
1.87-1.912.91014490.189194.6
1.91-1.963.212.115170.161195.2
1.96-2.023.41415180.146196.9
2.02-2.073.715.615320.133197
2.07-2.143.918.315200.115197
2.14-2.224.118.415060.103197.2
2.22-2.314.219.315560.098197.7
2.31-2.414.319.215460.091197.7
2.41-2.544.419.715030.085197.9
2.54-2.74.422.915480.075198.1
2.7-2.914.42215430.07198.3
2.91-3.24.423.115830.061198.7
3.2-3.664.427.215370.054198.7
3.66-4.614.331.415550.046198.9
4.61-504.330.415590.04199

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_336)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FQW

1fqw


Resolution: 1.697→24.805 Å / SU ML: 0.2 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2087 1909 6.82 %random
Rwork0.1738 ---
obs0.1762 27975 88.64 %-
all-31472 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.877 Å2 / ksol: 0.348 e/Å3
Displacement parametersBiso mean: 34.42 Å2
Baniso -1Baniso -2Baniso -3
1-4.9029 Å211.8633 Å26.7736 Å2
2---1.2467 Å27.5986 Å2
3----3.6562 Å2
Refinement stepCycle: LAST / Resolution: 1.697→24.805 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1954 0 36 331 2321
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072083
X-RAY DIFFRACTIONf_angle_d1.0342814
X-RAY DIFFRACTIONf_dihedral_angle_d13.381794
X-RAY DIFFRACTIONf_chiral_restr0.068323
X-RAY DIFFRACTIONf_plane_restr0.004361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6966-1.7390.2388860.1731289X-RAY DIFFRACTION60
1.739-1.7860.23771060.19151424X-RAY DIFFRACTION68
1.786-1.83850.25331190.18591597X-RAY DIFFRACTION77
1.8385-1.89790.21421390.18221802X-RAY DIFFRACTION85
1.8979-1.96570.26031430.18091881X-RAY DIFFRACTION89
1.9657-2.04430.2371270.19311908X-RAY DIFFRACTION91
2.0443-2.13730.2431420.18331971X-RAY DIFFRACTION93
2.1373-2.24990.21561540.17821944X-RAY DIFFRACTION93
2.2499-2.39080.22771420.18632015X-RAY DIFFRACTION96
2.3908-2.57520.25541480.19341997X-RAY DIFFRACTION96
2.5752-2.8340.23021440.1862036X-RAY DIFFRACTION97
2.834-3.24340.19851580.18062036X-RAY DIFFRACTION98
3.2434-4.08330.18641500.15352087X-RAY DIFFRACTION98
4.0833-24.80740.1681510.15682079X-RAY DIFFRACTION99

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