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- PDB-1tmw: Solution structure of Human Coactosin Like Protein D123N -

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Basic information

Entry
Database: PDB / ID: 1tmw
TitleSolution structure of Human Coactosin Like Protein D123N
ComponentsCoactosin-like protein
KeywordsPROTEIN BINDING / Coactosin-like protein
Function / homology
Function and homology information


site of polarized growth / regulation of actin filament polymerization / cortical actin cytoskeleton / defense response to fungus / actin filament / actin filament binding / actin binding / secretory granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation ...site of polarized growth / regulation of actin filament polymerization / cortical actin cytoskeleton / defense response to fungus / actin filament / actin filament binding / actin binding / secretory granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / enzyme binding / extracellular exosome / extracellular region / nucleus / cytosol
Similarity search - Function
Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / Severin / Severin / ADF-H/Gelsolin-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Coactosin-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics
AuthorsDai, H. / Wu, J. / Xu, Y. / Tang, Y. / Ding, H. / Shi, Y.
CitationJournal: To be Published
Title: Study on Solution Structure and Its binding function to F-actin
Authors: Dai, H. / Wu, J. / Xu, Y. / Tang, Y. / Ding, H. / Shi, Y.
History
DepositionJun 11, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 28, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: 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: Coactosin-like protein


Theoretical massNumber of molelcules
Total (without water)16,9051
Polymers16,9051
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 300structures with the lowest energy
RepresentativeModel #4closest to the average

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Components

#1: Protein Coactosin-like protein


Mass: 16904.936 Da / Num. of mol.: 1 / Mutation: D123N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q14019

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1213D 13C-separated NOESY
1323D 15N-separated NOESY
1432D NOESY
1513D CBCANH
1613D CBCA(CO)NH
1713D HNCO
1813D HNCA
1913D HBHA(CBCACO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM Human Coactosin Like Protein(D123N) U-15N, 13C; 50mM phosphate buffer, 50mM NaCl; 90% H2O, 10% D2O90% H2O/10% D2O
21.5mM Human Coactosin Like Protein(D123N) U-15N; 50mM phosphate buffer, 50mM NaCl; 90% H2O, 10% D2O90% H2O/10% D2O
31.5mM Human Coactosin Like Protein(D123N); 50mM phosphate buffer, 50mM NaCl; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 50mM NaH2PO4, 50mM NaCl / pH: 5.0 / Pressure: 1 atm / Temperature: 296 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.2F. Delagliodata analysis
Sparky3T.D. Goddard and D.G. Knellerdata analysis
CNS1.1A.T. Brunger, P.D. Adams, G.M. Clore, et. al.structure solution
CSI1David S. Wishartdata analysis
MOLMOL2K.2Koradistructure solution
MOLMOL2K.2Koradirefinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 20

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