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- PDB-1dv9: STRUCTURAL CHANGES ACCOMPANYING PH-INDUCED DISSOCIATION OF THE B-... -

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Basic information

Entry
Database: PDB / ID: 1dv9
TitleSTRUCTURAL CHANGES ACCOMPANYING PH-INDUCED DISSOCIATION OF THE B-LACTOGLOBULIN DIMER
ComponentsBETA-LACTOGLOBULIN
KeywordsTRANSPORT PROTEIN / Beta-lactoglobulin / beta-barrel / low pH structure / triple resonance experiments
Function / homology
Function and homology information


retinol binding / long-chain fatty acid binding / extracellular region / identical protein binding
Similarity search - Function
Beta-lactoglobulin / Lipocalin / Lipocalin family conserved site / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesBos taurus (domestic cattle)
MethodSOLUTION NMR / simulated annealing
AuthorsUhrinova, S. / Smith, M.H. / Jameson, G.B. / Uhrin, D. / Sawyer, L. / Barlow, P.N.
Citation
Journal: Biochemistry / Year: 2000
Title: Structural changes accompanying pH-induced dissociation of the beta-lactoglobulin dimer.
Authors: Uhrinova, S. / Smith, M.H. / Jameson, G.B. / Uhrin, D. / Sawyer, L. / Barlow, P.N.
#1: Journal: Protein Expr.Purif. / Year: 1998
Title: Isotopically Labelled Bovine Beta-lactoglobulin Expressed in P. pastoris
Authors: Denton, H. / Smith, M. / Husi, H. / Uhrin, D. / Barlow, P.N. / Batt, C.A. / Sawyer, L.
#2: Journal: J.Biomol.NMR / Year: 1998
Title: Complete Assignment of 1H, 13C and 15N Chemical Shifts for Bovine Beta-lactoglobulin: Secondary Structure and Topology of the Native State is Retained in a Partially Unfolded Form.
Authors: Uhrinova, S. / Uhrin, D. / Denton, H. / Smith, M. / Sawyer, L. / Barlow, P.N.
History
DepositionJan 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-LACTOGLOBULIN


Theoretical massNumber of molelcules
Total (without water)18,3951
Polymers18,3951
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)21 / 60lowest total energy
RepresentativeModel #14closest to the average

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Components

#1: Protein BETA-LACTOGLOBULIN


Mass: 18395.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SMALL PROTEIN FOUND IN THE WHEY OF MILK OF RUMINANTS AND OTHER SPECIES
Source: (gene. exp.) Bos taurus (domestic cattle)
Description: P.PASTORIS GS115/HIS+BLG/MUT+ CONTAINING PPIC9; PPIC9 DERIVED FROM PTTQ18BLG BY PCR
Variant: A / Plasmid: PPIC9 / Production host: Pichia pastoris (fungus) / References: UniProt: P02754
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: The structure was determined using triple resonance NMR spectra

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Sample preparation

DetailsContents: 1mM B-lactoglobuline-15N,13C; 50mM phosphate buffer; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: not known / pH: 2.7 / Pressure: ambient / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Felix97Molecular Simulationsprocessing
XEASY1995Bartels el al.processing
X-PLORARIANilges el al.structure solution
CNS0.9Brunger et al.structure solution
CNS0.9Brunger et al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 2715 restraints, out of which 77 are hydrogen bonds and 110 are torsion angles
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: lowest total energy / Conformers calculated total number: 60 / Conformers submitted total number: 21

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