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- PDB-1joy: SOLUTION STRUCTURE OF THE HOMODIMERIC DOMAIN OF ENVZ FROM ESCHERI... -

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Entry
Database: PDB / ID: 1joy
TitleSOLUTION STRUCTURE OF THE HOMODIMERIC DOMAIN OF ENVZ FROM ESCHERICHIA COLI BY MULTI-DIMENSIONAL NMR.
ComponentsPROTEIN (ENVZ_ECOLI)
KeywordsTRANSFERASE / HISTIDINE KINASE / SENSORY TRANSDUCTION / OSMOLARITY SENSOR PROTEIN / INNER MEMBRANE / PHOSPHORYLATION
Function / homology
Function and homology information


response to osmotic stress / histidine kinase / phosphorelay sensor kinase activity / phosphoprotein phosphatase activity / phosphorelay signal transduction system / outer membrane-bounded periplasmic space / protein autophosphorylation / membrane => GO:0016020 / phosphorylation / signal transduction ...response to osmotic stress / histidine kinase / phosphorelay sensor kinase activity / phosphoprotein phosphatase activity / phosphorelay signal transduction system / outer membrane-bounded periplasmic space / protein autophosphorylation / membrane => GO:0016020 / phosphorylation / signal transduction / protein homodimerization activity / ATP binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal ...Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Sensor histidine kinase EnvZ / Sensor histidine kinase EnvZ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsTomomori, C. / Tanaka, T. / Dutta, R. / Park, H. / Saha, S.K. / Zhu, Y. / Ishima, R. / Liu, D. / Tong, K.I. / Kurokawa, H. ...Tomomori, C. / Tanaka, T. / Dutta, R. / Park, H. / Saha, S.K. / Zhu, Y. / Ishima, R. / Liu, D. / Tong, K.I. / Kurokawa, H. / Qian, H. / Inouye, M. / Ikura, M.
Citation
Journal: Nat.Struct.Biol. / Year: 1999
Title: Solution structure of the homodimeric core domain of Escherichia coli histidine kinase EnvZ.
Authors: Tomomori, C. / Tanaka, T. / Dutta, R. / Park, H. / Saha, S.K. / Zhu, Y. / Ishima, R. / Liu, D. / Tong, K.I. / Kurokawa, H. / Qian, H. / Inouye, M. / Ikura, M.
#1: Journal: Nature / Year: 1998
Title: NMR Structure of the Histidine Kinase Domain of the E.coli Osmosensor EnvZ.
History
DepositionDec 28, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 12, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (ENVZ_ECOLI)
B: PROTEIN (ENVZ_ECOLI)


Theoretical massNumber of molelcules
Total (without water)15,1872
Polymers15,1872
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 100LEAST RESTRAINT VIOLATION
RepresentativeModel #7

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Components

#1: Protein PROTEIN (ENVZ_ECOLI) / EC 2.7.3.-


Mass: 7593.671 Da / Num. of mol.: 2 / Fragment: RESIDUES 223-289
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P02933, UniProt: P0AEJ4*PLUS, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C- LABELED OR 13C/15N-LABELED ENVZ (223-289).

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Sample preparation

Sample conditionspH: 7.2 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITY PLUS 500VarianUNITY PLUS 5005001
Varian UNITY 600VarianUNITY 6006002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
NMRPipestructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 100 / Conformers submitted total number: 21

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