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- PDB-2lbh: Solution Structure of the Dimeric Form of a Unliganded Bovine Neu... -

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Basic information

Entry
Database: PDB / ID: 2lbh
TitleSolution Structure of the Dimeric Form of a Unliganded Bovine Neurophysin, Minimized Average Structure
ComponentsNeurophysin 1
KeywordsPeptide binding protein / hormone / Dimerization
Function / homology
Function and homology information


Vasopressin-like receptors / oxytocin receptor binding / neurohypophyseal hormone activity / V1A vasopressin receptor binding / neuropeptide hormone activity / G alpha (q) signalling events / secretory granule / response to estrogen / extracellular space
Similarity search - Function
Neurophysin II; Chain A / Neurohypophysial hormone domain / Neurohypophysial hormone / Neurohypophysial hormone, conserved site / Neurohypophysial hormone domain superfamily / Neurohypophysial hormones, C-terminal Domain / Neurohypophysial hormones, N-terminal Domain / Neurohypophysial hormones signature. / Neurohypophysial hormones / Sandwich / Mainly Beta
Similarity search - Domain/homology
Oxytocin-neurophysin 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodSOLUTION NMR / simulated annealing
Model detailsminimized average structure, model 1
Model type detailsminimized average
AuthorsLee, H. / Naik, M. / Nguyen, T. / Bracken, C. / Breslow, E.
CitationJournal: To be Published
Title: Structural Basis of the Dimerization-Induced Increase in Neurophysin-Hormone Affinity: Interplay of Inter-Domain and Inter-Subunit Interactions
Authors: Lee, H. / Naik, M. / Bracken, C. / Breslow, E.
History
DepositionMar 31, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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 / pdbx_nmr_software / pdbx_nmr_spectrometer
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neurophysin 1
B: Neurophysin 1


Theoretical massNumber of molelcules
Total (without water)18,5912
Polymers18,5912
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 / 100structures with the least restraint violations
RepresentativeModel #1minimized average structure

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Components

#1: Protein Neurophysin 1


Mass: 9295.475 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: OXT / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de)plys S / References: UniProt: P01175
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCA
1413D HN(CO)CA
1513D HN(CA)CB
1613D HNHA
1713D HNCO
1813D 1H-15N NOESY
1913D 1H-13C NOESY
11013D (H)CCH-TOCSY
31112D 1H-15N HSQC
21212D 1H-15N HSQC

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Sample preparation

DetailsContents: 1 mM [U-100% 15N] protein, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: protein-1 / Isotopic labeling: [U-100% 15N]
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
102.7ambient 308 K
202.7ambient 298 K
310mM 0.15mM 2.7ambient 314 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE7003

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Processing

NMR software
NameVersionDeveloperClassification
CNSSOLVE1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
ARIA1Linge, O'Donoghue and Nilgesprocessing
NMRPipe1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
SparkyGoddarddata analysis
ProcheckNMRLaskowski and MacArthurdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1562
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 21

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