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- PDB-5xht: The PHD finger of human Kiaa1045 protein -

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Basic information

Entry
Database: PDB / ID: 5xht
TitleThe PHD finger of human Kiaa1045 protein
ComponentsPHD finger protein 24
KeywordsMETAL BINDING PROTEIN / PHD finger / Zinc Finger
Function / homology
Function and homology information


transcription corepressor activity / synaptic vesicle membrane / glutamatergic synapse / nucleus / cytoplasm
Similarity search - Function
KIAA1045, RING finger / KIAA1045 RING finger / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger, FYVE/PHD-type / EF-hand domain pair / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
PHD finger protein 24
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMiyamoto, K.
CitationJournal: Protein Sci. / Year: 2018
Title: Solution structure of the PHD finger from the human KIAA1045 protein
Authors: Miyamoto, K. / Yamashita, A. / Saito, K.
History
DepositionApr 24, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHD finger protein 24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9903
Polymers6,8591
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: the experimental cystein modification
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area100 Å2
ΔGint-39 kcal/mol
Surface area4650 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein PHD finger protein 24


Mass: 6858.710 Da / Num. of mol.: 1 / Fragment: UNP residues 131-190 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UPV7
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentSample state: isotropic / Type: 3D NOESY

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Sample preparation

DetailsType: solution / Contents: 1 mM U-13C;15N PHD finger, 90% H2O/10% D2O / Details: 20 mM Tris-HCl buffer, 50 mM NaCl, 1 mM DTT / Label: 13C 15N / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: PHD finger / Isotopic labeling: U-13C;15N
Sample conditionsIonic strength: 70 mM / Label: conditions_1 / pH: 6.9 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
NMRViewJohnson, One Moon Scientificdata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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