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

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Basic information

Entry
Database: PDB / ID: 3olx
TitleStructural and functional effects of substitution at position T+1 in CheY: CheYA88S-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: 2.1 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_alt_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_alt_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)29,31017
Polymers28,2572
Non-polymers1,05415
Water5,423301
1
A: Chemotaxis protein CheY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7399
Polymers14,1281
Non-polymers6108
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chemotaxis protein CheY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5728
Polymers14,1281
Non-polymers4437
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.687, 53.759, 160.013
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: 14128.332 Da / Num. of mol.: 2 / Mutation: A88S
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 , 6 types, 316 molecules

#2: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


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


Mass: 54.938 Da / Num. of mol.: 5 / 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-MG / MAGNESIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 301 / 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: 4.09 Å3/Da / Density % sol: 69.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Ammonium Sulfate 2.4 M Glycerol 5% (v/v) Tris 100 mM pH 7.5-8.5 MnCl2 20mM BeCl2 1mM NaF 10mM 7.2 mg/mL CheY A88S 2-15-10 , VAPOR DIFFUSION, HANGING DROP, temperature 298K
PH range: 7.5-8.5

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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: 2.1→50 Å / Num. all: 28356 / Num. obs: 28021 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 36.86 Å2 / Rsym value: 0.116 / Net I/σ(I): 16.6
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
2.1-2.145.92.913720.62198.5
2.14-2.186.33.313760.557198.1
2.18-2.226.74.313410.487198.5
2.22-2.266.85.513780.413197.5
2.26-2.3175.713600.41198.5
2.31-2.376.96.913650.346196.9
2.37-2.4278.113670.299198.8
2.42-2.496.99.313740.272198.5
2.49-2.567.110.913950.232198.6
2.56-2.657.112.313700.212198.9
2.65-2.747.114.714090.178199.3
2.74-2.857.216.713880.151199.4
2.85-2.987.216.513990.143199.3
2.98-3.147.217.714050.13199.6
3.14-3.337.217.914220.123199.5
3.33-3.597.117.314180.116199.6
3.59-3.95717.414220.11199.6
3.95-4.526.916.214590.098199.7
4.52-5.7718.814520.089199.5
5.7-506.522.815490.078198.1

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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: 2.1→26.879 Å / SU ML: 0.29 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2299 1427 5.34 %random
Rwork0.1891 ---
obs0.1913 26698 95.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.276 Å2 / ksol: 0.339 e/Å3
Displacement parametersBiso mean: 40.97 Å2
Baniso -1Baniso -2Baniso -3
1-1.9836 Å2-0 Å20 Å2
2---3.3752 Å2-0 Å2
3---1.3916 Å2
Refinement stepCycle: LAST / Resolution: 2.1→26.879 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1956 0 53 301 2310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072078
X-RAY DIFFRACTIONf_angle_d1.0842798
X-RAY DIFFRACTIONf_dihedral_angle_d13.293796
X-RAY DIFFRACTIONf_chiral_restr0.068317
X-RAY DIFFRACTIONf_plane_restr0.004360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.17510.32381320.2792289X-RAY DIFFRACTION88
2.1751-2.26210.28231410.2572322X-RAY DIFFRACTION90
2.2621-2.3650.32651320.24442388X-RAY DIFFRACTION92
2.365-2.48960.2991440.23912458X-RAY DIFFRACTION95
2.4896-2.64550.29281330.23262532X-RAY DIFFRACTION96
2.6455-2.84950.29161550.22382573X-RAY DIFFRACTION98
2.8495-3.13590.27421490.21942587X-RAY DIFFRACTION99
3.1359-3.58870.22031380.1772661X-RAY DIFFRACTION100
3.5887-4.51790.15991470.13852662X-RAY DIFFRACTION100
4.5179-26.88170.18641560.16012799X-RAY DIFFRACTION99

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