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

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Basic information

Entry
Database: PDB / ID: 3oly
TitleStructural and functional effects of substitution at position T+1 in CheY: CheYA88M-BeF3-Mn 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 / internal peptidyl-lysine acetylation / thermotaxis / regulation of chemotaxis / bacterial-type flagellum / 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 / internal peptidyl-lysine acetylation / thermotaxis / regulation of chemotaxis / bacterial-type flagellum / phosphorelay response regulator activity / acetyltransferase activity / phosphorelay signal transduction system / chemotaxis / magnesium ion binding / signal transduction / cytoplasm / cytosol
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: 2.05 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.pdbx_ptnr1_label_alt_id / _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)29,36316
Polymers28,3452
Non-polymers1,01814
Water5,819323
1
A: Chemotaxis protein CheY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6808
Polymers14,1721
Non-polymers5077
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chemotaxis protein CheY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6848
Polymers14,1721
Non-polymers5117
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.445, 53.547, 161.082
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Chemotaxis protein CheY


Mass: 14172.451 Da / Num. of mol.: 2 / Mutation: A88M
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

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Non-polymers , 5 types, 337 molecules

#2: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 4.07 Å3/Da / Density % sol: 69.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Ammonium Sulfate 2.4 M Glycerol 2.5% (v/v) Tris 100 mM pH 8.0 MnCl2 20mM BeCl2 1mM NaF 10mM 4.8 mg/mL CheY A88M 1-10-10, 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: Mar 24, 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: 2.05→50 Å / Num. all: 30591 / Num. obs: 30464 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 35.35 Å2 / Rsym value: 0.114 / Net I/σ(I): 15.7
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
2.05-2.096.22.715040.6731100
5.56-506.616.916780.075198.8
4.42-5.56719.215950.087199.7
3.86-4.427.116.815460.102199.9
3.51-3.867.215.815560.111100
3.25-3.517.216.415380.1091100
3.06-3.257.316.715260.1191100
2.91-3.067.317.715450.1281100
2.78-2.917.316.415270.141100
2.68-2.787.315.915080.1561100
2.58-2.687.313.714900.1821100
2.5-2.587.312.215370.1991100
2.43-2.57.21115000.2321100
2.37-2.437.31014980.255199.9
2.31-2.377.28.315230.2991100
2.26-2.317.27.314760.3371100
2.21-2.267.26.515430.3661100
2.16-2.217.1514790.4511100
2.12-2.1674.314860.4851100
2.09-2.126.73.415090.5781100

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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 3MYY

3myy


Resolution: 2.05→26.722 Å / SU ML: 0.26 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2124 1534 5.34 %random
Rwork0.1797 ---
obs0.1815 28710 96.23 %-
all-29834 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.447 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 40.37 Å2
Baniso -1Baniso -2Baniso -3
1--2.7844 Å20 Å20 Å2
2--2.2832 Å2-0 Å2
3---0.5012 Å2
Refinement stepCycle: LAST / Resolution: 2.05→26.722 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1956 0 49 323 2328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072093
X-RAY DIFFRACTIONf_angle_d1.0632820
X-RAY DIFFRACTIONf_dihedral_angle_d12.618809
X-RAY DIFFRACTIONf_chiral_restr0.072319
X-RAY DIFFRACTIONf_plane_restr0.004363
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.11610.36011210.28282241X-RAY DIFFRACTION89
2.1161-2.19170.27751360.24342281X-RAY DIFFRACTION91
2.1917-2.27950.24941360.22472353X-RAY DIFFRACTION93
2.2795-2.38310.27451360.21392418X-RAY DIFFRACTION95
2.3831-2.50870.25861400.21592444X-RAY DIFFRACTION96
2.5087-2.66570.29091420.21472474X-RAY DIFFRACTION98
2.6657-2.87130.27831410.21552488X-RAY DIFFRACTION98
2.8713-3.15990.23131440.20862570X-RAY DIFFRACTION99
3.1599-3.61620.19471400.16322565X-RAY DIFFRACTION100
3.6162-4.55230.14951420.12772606X-RAY DIFFRACTION100
4.5523-26.72480.17021560.1562736X-RAY DIFFRACTION99

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