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- PDB-1i5n: Crystal structure of the P1 domain of CheA from Salmonella typhimurium -

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Basic information

Entry
Database: PDB / ID: 1i5n
TitleCrystal structure of the P1 domain of CheA from Salmonella typhimurium
ComponentsCHEMOTAXIS PROTEIN CHEA
KeywordsTRANSFERASE / Four-helix bundle
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / chemotaxis / ATP binding / cytoplasm
Similarity search - Function
CheY binding / CheY binding / HPT domain / Histidine kinase CheA-like, homodimeric domain / CheY-binding domain of CheA / Histidine kinase CheA-like, homodimeric domain superfamily / Signal transducing histidine kinase, homodimeric domain / Signal transducing histidine kinase, homodimeric domain / : / CheW-like domain profile. ...CheY binding / CheY binding / HPT domain / Histidine kinase CheA-like, homodimeric domain / CheY-binding domain of CheA / Histidine kinase CheA-like, homodimeric domain superfamily / Signal transducing histidine kinase, homodimeric domain / Signal transducing histidine kinase, homodimeric domain / : / CheW-like domain profile. / CheW-like domain / CheW-like domain superfamily / CheW-like domain / Two component signalling adaptor domain / Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Four Helix Bundle (Hemerythrin (Met), subunit A) / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chemotaxis protein CheA
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.14 Å
AuthorsMourey, L. / Da Re, S. / Pedelacq, J.-D. / Tolstyk, T. / Faurie, C. / Guillet, V. / Stock, J.B. / Samama, J.-P.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: Crystal structure of the CheA histidine phosphotransfer domain that mediates response regulator phosphorylation in bacterial chemotaxis
Authors: Mourey, L. / Da Re, S. / Pedelacq, J.-D. / Tolstykh, T. / Faurie, C. / Guillet, V. / Stock, J.B. / Samama, J.-P.
#1: Journal: MICROBES INFECT. / Year: 2001
Title: The molecular puzzle of two-component signaling cascades
Authors: Foussard, M. / Cabantous, S. / Pedelacq, J.-D. / Guillet, V. / Tranier, S. / Mourey, L. / Birck, C. / Samama, J.
History
DepositionFeb 28, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _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 CHEA
B: CHEMOTAXIS PROTEIN CHEA
C: CHEMOTAXIS PROTEIN CHEA
D: CHEMOTAXIS PROTEIN CHEA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7075
Polymers67,6114
Non-polymers961
Water3,873215
1
A: CHEMOTAXIS PROTEIN CHEA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9992
Polymers16,9031
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CHEMOTAXIS PROTEIN CHEA


Theoretical massNumber of molelcules
Total (without water)16,9031
Polymers16,9031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: CHEMOTAXIS PROTEIN CHEA


Theoretical massNumber of molelcules
Total (without water)16,9031
Polymers16,9031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: CHEMOTAXIS PROTEIN CHEA


Theoretical massNumber of molelcules
Total (without water)16,9031
Polymers16,9031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.95, 88.72, 115.82
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer. There are four such monomers in the asymmetric unit.

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Components

#1: Protein
CHEMOTAXIS PROTEIN CHEA


Mass: 16902.771 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-138
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: CHEA / Production host: Escherichia coli (E. coli)
References: UniProt: P09384, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.06 Å3/Da / Density % sol: 39.9 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 5
Details: POLYETHYLENE GLYCOL 2000 MONOMETHYL ETHER, AMMONIUM SULFATE, SODIUM ACETATE, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal grow
*PLUS
pH: 7.5 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17 mg/mlprotein1drop
225 mMTris-HCl1reservoir
325 mM1reservoirNaCl
43.5 mMEDTA1reservoir
515 mMbeta-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9802, 0.9300, 0.9805
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 18, 1999
RadiationMonochromator: DOUBLE CRYSTAL FOCUSSING MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.98021
20.931
30.98051
ReflectionResolution: 2.14→35.3 Å / Num. all: 206627 / Num. obs: 31247 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 6.8
Reflection shellResolution: 2.14→2.26 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.167 / % possible all: 91.3
Reflection
*PLUS
Num. measured all: 206627
Reflection shell
*PLUS
% possible obs: 91.3 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
SHARPphasing
AMoREphasing
CNS0.9refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.14→35.3 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1548 5 %RANDOM
Rwork0.21 ---
all0.212 31179 --
obs0.212 31179 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.9 Å2 / ksol: 0.368 e/Å3
Displacement parametersBiso mean: 23.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.14→35.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4024 0 5 215 4244
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.91.5
X-RAY DIFFRACTIONc_mcangle_it2.62
X-RAY DIFFRACTIONc_scbond_it3.442
X-RAY DIFFRACTIONc_scangle_it4.52.5
LS refinement shellResolution: 2.14→2.28 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.299 245 5.3 %
Rwork0.257 4410 -
obs--88.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.param
X-RAY DIFFRACTION3ion.param
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 35.3 Å / Num. reflection obs: 29631 / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.21 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79
X-RAY DIFFRACTIONc_mcbond_it1.91.5
X-RAY DIFFRACTIONc_scbond_it3.442
X-RAY DIFFRACTIONc_mcangle_it2.62
X-RAY DIFFRACTIONc_scangle_it4.52.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.299 / % reflection Rfree: 5.3 % / Rfactor Rwork: 0.257

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