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- PDB-1jbi: NMR structure of the LCCL domain -

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Basic information

Entry
Database: PDB / ID: 1jbi
TitleNMR structure of the LCCL domain
Componentscochlin
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein
Function / homology
Function and homology information


positive regulation of innate immune response / collagen binding / sensory perception of sound / regulation of cell shape / collagen-containing extracellular matrix / defense response to bacterium
Similarity search - Function
LCCL-like domain / LCCL domain / LCCL domain / LCCL domain profile. / LCCL / LCCL domain superfamily / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. ...LCCL-like domain / LCCL domain / LCCL domain / LCCL domain profile. / LCCL / LCCL domain superfamily / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics,simulated annealing
AuthorsLiepinsh, E. / Trexler, M. / Kaikkonen, A. / Weigelt, J. / Banyai, L. / Patthy, L. / Otting, G.
CitationJournal: EMBO J. / Year: 2001
Title: NMR structure of the LCCL domain and implications for DFNA9 deafness disorder.
Authors: Liepinsh, E. / Trexler, M. / Kaikkonen, A. / Weigelt, J. / Banyai, L. / Patthy, L. / Otting, G.
History
DepositionJun 5, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2001Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cochlin


Theoretical massNumber of molelcules
Total (without water)10,6101
Polymers10,6101
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)20 / 50structures with the lowest energy,target function
RepresentativeModel #15closest to the average

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Components

#1: Protein cochlin / COCH-5B2


Mass: 10609.979 Da / Num. of mol.: 1 / Fragment: LCCL module
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: M13mp18 / Plasmid: pmed23 / Production host: Escherichia coli (E. coli) / Strain (production host): JM 109 / References: UniProt: O43405

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY,2D ROESY, 2D DQF-COSY,2D TOCSY
2223D-15N-separated-NOESY,3D-15N-separated-TOCSY, 1H-15N-HSQC
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM LCCL; 90% H2O, 10% D2O90% H2O/10% D2O
23mg/ml LCCL U-15N; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.1 4.9 ambient 301 K
20.1 4.9 ambient 301 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Varian UNITYVarianUNITY8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.5Brukercollection
PROSA3.4Guntertprocessing
XEASY2.6Guntertdata analysis
DYANA1.5Guntertstructure solution
OPAL2.2Luginbuhlrefinement
RefinementMethod: torsion angle dynamics,simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 2532 restraints, 1193 are NOE-derived distance constraints, 270 dihedral angle restraints and 69 residual dipolar coupling restraints
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy,target function
Conformers calculated total number: 50 / Conformers submitted total number: 20

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