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- PDB-2l7i: The solution structure of the HAMP domain of the hypothetical tra... -

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Basic information

Entry
Database: PDB / ID: 2l7i
TitleThe solution structure of the HAMP domain of the hypothetical transmembrane receptor Af1503 (A291F variant)
ComponentsUncharacterized protein
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


histidine kinase / phosphorelay signal transduction system / kinase activity / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
HAMP domain in histidine kinase / : / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesArchaeoglobus fulgidus (archaea)
MethodSOLUTION NMR / simulated annealing
Model detailsminimized average, model 1
AuthorsColes, M. / Hulko, M. / Martin, J. / Lupas, A.N.
Citation
Journal: Structure / Year: 2011
Title: The Mechanisms of HAMP-Mediated Signaling in Transmembrane Receptors.
Authors: Ferris, H.U. / Dunin-Horkawicz, S. / Mondejar, L.G. / Hulko, M. / Hantke, K. / Martin, J. / Schultz, J.E. / Zeth, K. / Lupas, A.N. / Coles, M.
#1: Journal: Cell(Cambridge,Mass.) / Year: 2006
Title: The HAMP domain structure implies helix rotation in transmembrane signaling.
Authors: Hulko, M. / Berndt, F. / Gruber, M. / Linder, J.U. / Truffault, V. / Schultz, A. / Martin, J. / Schultz, J.E. / Lupas, A.N. / Coles, M.
History
DepositionDec 9, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 8, 2023Group: Data collection / Database references
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.4May 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: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)12,9952
Polymers12,9952
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

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Components

#1: Protein Uncharacterized protein


Mass: 6497.419 Da / Num. of mol.: 2 / Fragment: HAMP domain residues 278-331 / Mutation: A291F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: af1503, AF_1503 / Production host: Escherichia coli (E. coli) / References: UniProt: O28769

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 1H-15N NOESY
1233D 1H-13C NOESY
1332D 13C-edited/12C-filtered NOESY
1412D 1H-1H NOESY
1533D CNH-NOESY
1623D NNH-NOESY
1733D HNCA
1833D (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM Af1503 HAMP (A921F), 20 mM phosphate buffer, 150 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 15N] Af1503 HAMP (A921F), 20 mM phosphate buffer, 150 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
30.5 mM [U-100% 13C; U-100% 15N] Af1503 HAMP (A921F), 0.5 mM Af1503 HAMP (A921F), 20 mM phosphate buffer, 150 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMAf1503 HAMP (A921F)-11
20 mMphosphate buffer-21
150 mMsodium chloride-31
1 mMAf1503 HAMP (A921F)-4[U-100% 15N]2
20 mMphosphate buffer-52
150 mMsodium chloride-62
0.5 mMAf1503 HAMP (A921F)-7[U-100% 13C; U-100% 15N]3
0.5 mMAf1503 HAMP (A921F)-83
20 mMphosphate buffer-93
150 mMsodium chloride-103
Sample conditionsIonic strength: 150 / pH: 7.2 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE9002

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3.11Goddarddata analysis
TopSpin2Bruker Biospincollection
TopSpin2Bruker Biospinprocessing
X-PLOR NIH2.9.7Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.9.7Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Refinement against a conformational database potential
NMR constraintsNOE constraints total: 874 / NOE intraresidue total count: 166 / NOE long range total count: 158 / NOE medium range total count: 212 / NOE sequential total count: 262 / Protein chi angle constraints total count: 70 / Protein other angle constraints total count: 28 / Protein phi angle constraints total count: 114 / Protein psi angle constraints total count: 108
NMR representativeSelection criteria: minimized average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 18 / Maximum lower distance constraint violation: 0.04 Å / Maximum torsion angle constraint violation: 0.3 ° / Maximum upper distance constraint violation: 0.07 Å
NMR ensemble rmsDistance rms dev: 0.011 Å / Distance rms dev error: 0.0005 Å

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