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- PDB-1bw5: THE NMR SOLUTION STRUCTURE OF THE HOMEODOMAIN OF THE RAT INSULIN ... -

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Basic information

Entry
Database: PDB / ID: 1bw5
TitleTHE NMR SOLUTION STRUCTURE OF THE HOMEODOMAIN OF THE RAT INSULIN GENE ENHANCER PROTEIN ISL-1, 50 STRUCTURES
ComponentsINSULIN GENE ENHANCER PROTEIN ISL-1
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / HOMEODOMAIN / LIM DOMAIN
Function / homology
Function and homology information


visceral motor neuron differentiation / spinal cord motor neuron cell fate specification / neuron fate specification / neuron fate commitment / retinal ganglion cell axon guidance / negative regulation of neuron differentiation / axonogenesis / sequence-specific double-stranded DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / metal ion binding / nucleus
Similarity search - Function
LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain ...LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Insulin gene enhancer protein ISL-2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing
AuthorsIppel, J.H. / Larsson, G. / Behravan, G. / Zdunek, J. / Lundqvist, M. / Schleucher, J. / Lycksell, P.-O. / Wijmenga, S.S.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: The solution structure of the homeodomain of the rat insulin-gene enhancer protein isl-1. Comparison with other homeodomains.
Authors: Ippel, H. / Larsson, G. / Behravan, G. / Zdunek, J. / Lundqvist, M. / Schleucher, J. / Lycksell, P.O. / Wijmenga, S.
#1: Journal: J.Biomol.NMR / Year: 1998
Title: 1H, 13C and 15N Assignment of the Isl-1 Homeodomain
Authors: Ippel, J.H. / Larsson, G. / Behravan, G. / Lundqvist, M. / Lycksell, P.O. / Schleucher, J. / Zdunek, J. / Wijmenga, S.S.
History
DepositionSep 29, 1998Processing site: BNL
Revision 1.0Jun 15, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_keywords.text / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INSULIN GENE ENHANCER PROTEIN ISL-1


Theoretical massNumber of molelcules
Total (without water)7,8941
Polymers7,8941
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)50 / 50LOW RESTRAINT ENERGY
RepresentativeModel #4

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Components

#1: Protein INSULIN GENE ENHANCER PROTEIN ISL-1 / ISL-1HD


Mass: 7893.507 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Organ: PANCREAS / References: UniProt: P50480

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-EDITED NOESY
12115N-EDITED TOCSY
13113C-EDITED NOESY
141TRIPLE RESONANCE EXPERIMENTS
NMR detailsText: THE STRUCTURE WAS DETERMINED USING 3D-EDITED NOESY AND TRIPLE RESONANCE SPECTRA ON UNIFORMLY LABELLED 15N AND UNIFORMLY LABELLED 13C, 15N SAMPLES OF ISL-1HD.

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Sample preparation

Sample conditionsIonic strength: 50 mM NA+ / pH: 6.0 / Temperature: 281 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX600 / Manufacturer: Bruker / Model: DRX600 / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XPLOR3.851BRUNGERrefinement
BRUKER UXNMRUXNMRstructure solution
XEASYstructure solution
X-PLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: LOW RESTRAINT ENERGY / Conformers calculated total number: 50 / Conformers submitted total number: 50

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