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- PDB-2lfr: Solution structure of the chimeric Af1503 HAMP- EnvZ DHp homodimer -

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Basic information

Entry
Database: PDB / ID: 2lfr
TitleSolution structure of the chimeric Af1503 HAMP- EnvZ DHp homodimer
ComponentsHAMP domain-containing protein, Osmolarity sensor protein EnzV chimera
KeywordsTRANSFERASE / transmembrane signaling / HAMP domain / histidine kinase / gearbox model
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / signal transduction / ATP binding / identical protein binding / membrane / metal ion binding / plasma membrane
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
HAMP domain-containing protein / Sensor histidine kinase EnvZ
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
Shigella flexneri (bacteria)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsColes, M. / Ferris, H.U. / Hulko, M. / Martin, J. / Lupas, A.N.
CitationJournal: Structure / Year: 2012
Title: Mechanism of regulation of receptor histidine kinases.
Authors: Ferris, H.U. / Dunin-Horkawicz, S. / Hornig, N. / Hulko, M. / Martin, J. / Schultz, J.E. / Zeth, K. / Lupas, A.N. / Coles, M.
History
DepositionJul 10, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2012Group: Database references
Revision 1.2Aug 18, 2021Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Source and taxonomy / Structure summary
Category: database_2 / entity ...database_2 / entity / entity_name_com / entity_src_gen / pdbx_nmr_exptl / pdbx_nmr_exptl_sample / pdbx_nmr_representative / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / struct / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_nmr_exptl.conditions_id / _pdbx_nmr_exptl.solution_id / _pdbx_nmr_exptl_sample.component / _pdbx_nmr_exptl_sample.isotopic_labeling / _pdbx_nmr_representative.selection_criteria / _pdbx_nmr_software.authors / _pdbx_nmr_software.name / _pdbx_nmr_software.version / _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model / _struct.pdbx_model_details / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HAMP domain-containing protein, Osmolarity sensor protein EnzV chimera
B: HAMP domain-containing protein, Osmolarity sensor protein EnzV chimera


Theoretical massNumber of molelcules
Total (without water)25,8552
Polymers25,8552
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)18 / 50structures with the least restraint violations
RepresentativeModel #1minimized average structure

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Components

#1: Protein HAMP domain-containing protein, Osmolarity sensor protein EnzV chimera / Sensor histidine kinase EnvZ


Mass: 12927.678 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (archaea), (gene. exp.) Shigella flexneri (bacteria)
Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
Gene: AF_1503, envZ, SF3423, S4340 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O28769, UniProt: P0AEJ5, histidine kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D HNCO
1223D HNCA
1323D CBCA(CO)NH
1423D CCH-TOCSY
1513D 1H-15N NOESY
1613D NNH NOESY
1723D 1H-13C NOESY
1823D CNH NOESY
1923D CCH NOESY
11022D 12C FILTERED/13C EDITED NOESY
11112D 12C/14N FILTERED 1H-1H NOESY
11213D HNHA

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.6 MM [U-100% 15N] HAMP-DHP, 12 MM PHOSPHATE BUFFER, 138 MM SODIUM CHLORIDE, 90% H2O/10% D2Osample_190% H2O/10% D2O
solution20.6 MM [U-100% 13C U-100% 15N] HAMP-DHP, 12 MM PHOSPHATE BUFFER, 138 MM SODIUM CHLORIDE, 90% H2O/ 10% D2Osample_290% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMHAMP-DHp[U-100% 15N]1
50 mMphosphate buffernatural abundance1
200 mMsodium chloridenatural abundance1
0.6 mMHAMP-DHp[U-100% 13C; U-100% 15N]2
50 mMphosphate buffernatural abundance2
200 mMsodium chloridenatural abundance2
Sample conditionsIonic strength: 0.150 / pH: 7.1 / Pressure: AMBIENT / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCE IIIBrukerAVANCE III8002
Bruker AVANCEBrukerAVANCE9003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.21Schwieters, Kuszewski, Tjandra and Clorerefinement
TopSpinBruker Biospinstructure solution
SparkyGoddardstructure solution
X-PLOR NIH2.21Schwieters, Kuszewski, Tjandra and Clorestructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: NON-BONDED POTENTIAL SUPPLEMENTED WITH CONFORMATIONAL DATABASE POTENTIAL
NMR constraintsProtein chi angle constraints total count: 138 / Protein other angle constraints total count: 78 / Protein phi angle constraints total count: 212 / Protein psi angle constraints total count: 202
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 18
NMR ensemble rmsDistance rms dev: 0.012 Å / Distance rms dev error: 0.005 Å

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