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- PDB-1ab6: STRUCTURE OF CHEY MUTANT F14N, V86T -

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Basic information

Entry
Database: PDB / ID: 1ab6
TitleSTRUCTURE OF CHEY MUTANT F14N, V86T
ComponentsCHEMOTAXIS PROTEIN CHEY
KeywordsCHEMOTAXIS / SENSORY TRANSDUCTION / PHOSPHORYLATION / FLAGELLAR ROT
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 / protein acetylation / 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
Chemotaxis protein CheY / Chemotaxis protein CheY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR / Resolution: 2.2 Å
AuthorsWilcock, D. / Pisabarro, M.T. / Lopez-Hernandez, E. / Serranno, L. / Coll, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Structure analysis of two CheY mutants: importance of the hydrogen-bond contribution to protein stability.
Authors: Wilcock, D. / Pisabarro, M.T. / Lopez-Hernandez, E. / Serrano, L. / Coll, M.
History
DepositionFeb 4, 1997Processing site: BNL
Revision 1.0Feb 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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


Theoretical massNumber of molelcules
Total (without water)27,2692
Polymers27,2692
Non-polymers00
Water73941
1
A: CHEMOTAXIS PROTEIN CHEY


Theoretical massNumber of molelcules
Total (without water)13,6351
Polymers13,6351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CHEMOTAXIS PROTEIN CHEY


Theoretical massNumber of molelcules
Total (without water)13,6351
Polymers13,6351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.070, 54.070, 91.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein CHEMOTAXIS PROTEIN CHEY / CHEY


Mass: 13634.692 Da / Num. of mol.: 2 / Mutation: F14N, V86T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PTZ18U (PHARMACIA) / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P06143, UniProt: P0AE67*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE CIS PROLINE AT 110 NECESSARY FOR ACTIVITY OF THE PROTEIN.

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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: 3.15 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 293 K / pH: 7.2
Details: THE PROTEIN WAS CRYSTALLIZED WITH 3.0M AMMONIUM SULFATE, PH7.2 AT 20C., temperature 293K
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.6-3.0 Mammonium sulfate1reservoir
20.7 mg/mlprotein1drop
31.7-2.0 Mammonium sulfate1drop
4Tris-HCl1reservoir
5Tris-HCl1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1995 / Details: SLITS
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→15 Å / Num. obs: 13544 / % possible obs: 86 % / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Biso Wilson estimate: 40.4 Å2 / Rmerge(I) obs: 0.048
Reflection shellResolution: 2.2→2.34 Å / Rmerge(I) obs: 0.29 / % possible all: 55.6
Reflection
*PLUS
Num. measured all: 25441
Reflection shell
*PLUS
% possible obs: 55.6 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.843refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR
Starting model: 3CHY

3chy


Resolution: 2.2→10 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: A POSTERIORI / σ(F): 2 / Details: RESOLUTION-DEPENDENT WEIGHTING
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1148 10.3 %RANDOM
Rwork0.192 ---
obs0.192 11179 74.2 %-
Displacement parametersBiso mean: 35.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1908 0 0 41 1949
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.25
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.841.5
X-RAY DIFFRACTIONx_mcangle_it4.412
X-RAY DIFFRACTIONx_scbond_it4.692
X-RAY DIFFRACTIONx_scangle_it7.072.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.364 153 11 %
Rwork0.293 1239 -
obs--55.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.25

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