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- PDB-6fvc: Protein environment affects the water-tryptophan binding mode. Mo... -

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Basic information

Entry
Database: PDB / ID: 6fvc
TitleProtein environment affects the water-tryptophan binding mode. Molecular dynamics simulations of Engrailed homeodomain mutants
ComponentsSegmentation polarity homeobox protein engrailed
KeywordsDNA BINDING PROTEIN / Engrailed Homeodomain / K52E mutation / DNA
Function / homology
Function and homology information


posterior compartment specification / analia development / anterior head segmentation / posterior head segmentation / anterior/posterior lineage restriction, imaginal disc / trunk segmentation / genital disc development / genital disc anterior/posterior pattern formation / spiracle morphogenesis, open tracheal system / wing disc anterior/posterior pattern formation ...posterior compartment specification / analia development / anterior head segmentation / posterior head segmentation / anterior/posterior lineage restriction, imaginal disc / trunk segmentation / genital disc development / genital disc anterior/posterior pattern formation / spiracle morphogenesis, open tracheal system / wing disc anterior/posterior pattern formation / wing disc morphogenesis / neuroblast fate determination / imaginal disc-derived wing vein specification / segment polarity determination / ventral midline development / compartment pattern specification / gonad development / axon guidance / RNA polymerase II transcription regulatory region sequence-specific DNA binding / neuron differentiation / DNA-binding transcription repressor activity, RNA polymerase II-specific / regulation of gene expression / negative regulation of neuron apoptotic process / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Homeobox domain engrailed / Homeobox engrailed, C-terminal / Homeobox engrailed-type, conserved site / Engrailed homeobox C-terminal signature domain / 'Homeobox' engrailed-type protein signature. / Helix-turn-helix motif / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain ...Homeobox domain engrailed / Homeobox engrailed, C-terminal / Homeobox engrailed-type, conserved site / Engrailed homeobox C-terminal signature domain / 'Homeobox' engrailed-type protein signature. / Helix-turn-helix motif / Homeobox domain, metazoa / 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
Segmentation polarity homeobox protein engrailed
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / simulated annealing
AuthorsTrosanova, Z. / Zachrdla, M. / Jansen, S. / Srb, P. / Zidek, L. / Kozelka, J.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science FoundationGF 14-14654S Czech Republic
CitationJournal: Phys Chem Chem Phys / Year: 2018
Title: Protein environment affects the water-tryptophan binding mode. MD, QM/MM, and NMR studies of engrailed homeodomain mutants.
Authors: Spackova, N. / Trosanova, Z. / Sebesta, F. / Jansen, S. / Burda, J.V. / Srb, P. / Zachrdla, M. / Zidek, L. / Kozelka, J.
History
DepositionMar 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Segmentation polarity homeobox protein engrailed


Theoretical massNumber of molelcules
Total (without water)7,6271
Polymers7,6271
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5730 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)3 / 100three representative structures for the conformational equilibrium along the torsion angle N-CA-CB-CG of asparagine N51
RepresentativeModel #1closest to the average

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Components

#1: Protein Segmentation polarity homeobox protein engrailed


Mass: 7626.657 Da / Num. of mol.: 1 / Mutation: K52E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: en, CG9015 / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / References: UniProt: P02836
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentSample state: anisotropic / Type: 2D 1H-1H NOESY

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Sample preparation

DetailsType: solution / Contents: 1 mM EnHD_K52E, 90% H2O/10% D2O / Label: 1H_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: EnHD_K52E / Isotopic labeling: natural abundance
Sample conditionsDetails: 100 mM NaCl 50 mM Sodium Acetate pH 5.7 / Ionic strength: 150 mM / Label: condition_1 / pH: 5.7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 850 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: three representative structures for the conformational equilibrium along the torsion angle N-CA-CB-CG of asparagine N51
Conformers calculated total number: 100 / Conformers submitted total number: 3

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