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- PDB-2hdl: Solution structure of Brak/CXCL14 -

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Basic information

Entry
Database: PDB / ID: 2hdl
TitleSolution structure of Brak/CXCL14
ComponentsSmall inducible cytokine B14
KeywordsCYTOKINE / CXCL14 / Brak / chemokine
Function / homology
Function and homology information


chemokine activity / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / cell-cell signaling / Golgi apparatus / signal transduction / extracellular space
Similarity search - Function
Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
C-X-C motif chemokine 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVEN
AuthorsPeterson, F.C. / Thorpe, J.A. / Harder, A.G. / Volkman, B.F. / Schwarze, S.R.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structural Determinants Involved in the Regulation of CXCL14/BRAK Expression by the 26 S Proteasome.
Authors: Peterson, F.C. / Thorpe, J.A. / Harder, A.G. / Volkman, B.F. / Schwarze, S.R.
History
DepositionJun 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Small inducible cytokine B14


Theoretical massNumber of molelcules
Total (without water)9,5001
Polymers9,5001
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Small inducible cytokine B14 / CXCL14 / Chemokine BRAK


Mass: 9500.201 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXCL14, NJAC, SCYB14 / Plasmid: pQE308HT / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009[pREP4] / References: UniProt: O95715
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1313D 13C-separated NOESY (AROMATIC)
NMR detailsText: ALL TRIPLE-RESONANCE AND NOESY SPECTRA WERE ACQUIRED USING A CRYOGENIC PROBE

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Sample preparation

DetailsContents: 1 mM CXCL14 U-15N, 13C; 100mM phosphate buffer, 150mM NaCl,95% H2O, 5% D2O
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 300 mM / pH: 6.5 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5collection
NMRPipe2004Delaglio, F., Grzesiek, S., Vuister, G.W., Zhu, G., Pfeifer, J., Bax, A.processing
SPSCAN1.1.0Glaser, R.W.data analysis
XEASY1.3Bartels, C, Xia, T.-H., Billeter, M., Guntert, P., Wuthrich, K.data analysis
GARANT2.1Bartels, C., Billeter, M., Guntert, P., Wuthrich, K.data analysis
CYANA2.1Herrmann, T., Guntert, P., Wuthrich, K.structure solution
XPLOR-NIH2.9.3Schwieters, C.D., Kuszewski, J.J, Tjandra, N., Clore, G.M.refinement
RefinementMethod: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVEN
Software ordinal: 1
Details: STRUCTURES ARE BASED ON A TOTAL OF 894 NOE CONSTRAINTS ( 366 INTRA, 186 SEQUENTIAL, 133 MEDIUM and 209 LONG RANGE CONSTRAINTS) AND 97 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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