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- PDB-1cb3: LOCAL INTERACTIONS DRIVE THE FORMATION OF NON-NATIVE STRUCTURE IN... -

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Basic information

Entry
Database: PDB / ID: 1cb3
TitleLOCAL INTERACTIONS DRIVE THE FORMATION OF NON-NATIVE STRUCTURE IN THE DENATURED STATE OF HUMAN ALPHA-LACTALBUMIN: A HIGH RESOLUTION STRUCTURAL CHARACTERIZATION OF A PEPTIDE MODEL IN AQUEOUS SOLUTION
ComponentsLCA
KeywordsMOLTEN GLOBULE STATE / PROTEIN FOLDING / NON-NATIVE INTERACTIONS / ALPHA- LACTALBUMIN
Function / homology
Function and homology information


Lactose synthesis / lactose synthase activity / lactose biosynthetic process / Golgi lumen / cell-cell signaling / lysozyme activity / defense response to bacterium / Golgi membrane / apoptotic process / calcium ion binding ...Lactose synthesis / lactose synthase activity / lactose biosynthetic process / Golgi lumen / cell-cell signaling / lysozyme activity / defense response to bacterium / Golgi membrane / apoptotic process / calcium ion binding / signal transduction / protein-containing complex / extracellular space
Similarity search - Function
Lactalbumin / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsDemarest, S.J. / Hua, Y. / Raleigh, D.P.
CitationJournal: Biochemistry / Year: 1999
Title: Local interactions drive the formation of nonnative structure in the denatured state of human alpha-lactalbumin: a high resolution structural characterization of a peptide model in aqueous solution.
Authors: Demarest, S.J. / Hua, Y. / Raleigh, D.P.
History
DepositionFeb 26, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jun 8, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: database_2 / entity ...database_2 / entity / pdbx_entity_src_syn / pdbx_nmr_ensemble / pdbx_nmr_exptl / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _pdbx_nmr_ensemble.conformer_selection_criteria / _pdbx_nmr_exptl.type / _pdbx_nmr_software.authors / _pdbx_nmr_software.version / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _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: LCA


Theoretical massNumber of molelcules
Total (without water)1,3271
Polymers1,3271
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / 200structures with the least restraint violations
RepresentativeModel #1

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Components

#1: Protein/peptide LCA


Mass: 1326.566 Da / Num. of mol.: 1 / Mutation: C11A / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / Source: (synth.) Homo sapiens (human) / References: UniProt: P00709

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111ROESY
121TOCSY
131DQF-COSY
141E.COSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING 1H NMR SPECTROSCOPY ON A CHEMICALLY SYNTHESIZED PEPTIDE CORRESPONDING TO RESIDUES 120-130 OF HUMAN ALPHA- LACTALBUMIN

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Sample preparation

Sample conditionspH: 2.8 / Pressure: 1 atm / Temperature: 283 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
X-PLOR3.851BRUNGERstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
Details: BOND LENGTHS (A) : 0.0035; BOND ANGLES (DEGREES) : 0.59; IMPROPER ANGLES (DEGREES) : 0.35; PARAMETER FILE 1 : PARALLHDG.PRO; TOPOLOGY FILE 1 : TOPALLHDG.PRO
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 40

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