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- PDB-1bxd: NMR STRUCTURE OF THE HISTIDINE KINASE DOMAIN OF THE E. COLI OSMOS... -

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Basic information

Entry
Database: PDB / ID: 1bxd
TitleNMR STRUCTURE OF THE HISTIDINE KINASE DOMAIN OF THE E. COLI OSMOSENSOR ENVZ
ComponentsPROTEIN (OSMOLARITY SENSOR PROTEIN (ENVZ))
KeywordsTRANSFERASE / HISTIDINE KINASE / OSMOSENSOR / HIS-ASP PHOSPHORELAY SYSTEM / SIGNAL TRANSDUCTION
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
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 ...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-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Sensor histidine kinase EnvZ / Sensor histidine kinase EnvZ
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodSOLUTION NMR
AuthorsTanaka, T. / Saha, S.K. / Tomomori, C. / Ishima, R. / Liu, D. / Tong, K.I. / Park, H. / Dutta, R. / Qin, L. / Swindells, M.B. ...Tanaka, T. / Saha, S.K. / Tomomori, C. / Ishima, R. / Liu, D. / Tong, K.I. / Park, H. / Dutta, R. / Qin, L. / Swindells, M.B. / Yamazaki, T. / Ono, A.M. / Kainosho, M. / Inouye, M. / Ikura, M.
CitationJournal: Nature / Year: 1998
Title: NMR structure of the histidine kinase domain of the E. coli osmosensor EnvZ.
Authors: Tanaka, T. / Saha, S.K. / Tomomori, C. / Ishima, R. / Liu, D. / Tong, K.I. / Park, H. / Dutta, R. / Qin, L. / Swindells, M.B. / Yamazaki, T. / Ono, A.M. / Kainosho, M. / Inouye, M. / Ikura, M.
History
DepositionOct 2, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 2, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (OSMOLARITY SENSOR PROTEIN (ENVZ))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9242
Polymers17,4181
Non-polymers5061
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / -
Representative

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Components

#1: Protein PROTEIN (OSMOLARITY SENSOR PROTEIN (ENVZ)) / ENVZ(290-450)


Mass: 17417.697 Da / Num. of mol.: 1 / Fragment: RESIDUES 290-450
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Species: Escherichia coli / Strain: BL21-DE3 / Cellular location: CYTOPLASM / Plasmid: PET11A / 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
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-1H HSQC
1211H-13C CT-HSQC
1311H-15N HMQC-J
1411H NOESY
1511H TOCSY
161(HB)CBCA(CO)NNH
171HN(CA)CB
181(HB)CBCACO(CA)HA
191HNCO
1101(H)CCH-TOCSY
111115N-EDITED TOCSY-HMQC
112115N-EDITED NOESY-HSQC
113113C-EDITED NOESY-HMQC
1141SIMULTANEOUS 13C/ 15N-EDITED NOESY-HMQC
115113C-FILTERED TOCSY
1161[13C/ F1]-EDITED [13C/F2]-FILTERED NOESY

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Sample preparation

Sample conditionspH: 7.0 / 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
Bruker DMX750BrukerDMX7507503

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Processing

NMR softwareName: X-PLOR / Version: 3.8.5.1 / Developer: BRUNGER / Classification: refinement
NMR ensembleConformers submitted total number: 20

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