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- PDB-8x1g: Human adenylate kinase 1 (hAK1) mutant-R97W -

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Basic information

Entry
Database: PDB / ID: 8x1g
TitleHuman adenylate kinase 1 (hAK1) mutant-R97W
ComponentsAdenylate kinase isoenzyme 1
KeywordsTRANSFERASE / adenylate kinase
Function / homology
Function and homology information


nucleoside-phosphate kinase / dAMP kinase activity / outer dense fiber / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / adenylate kinase / AMP kinase activity / nucleobase-containing small molecule interconversion / nucleoside-diphosphate kinase ...nucleoside-phosphate kinase / dAMP kinase activity / outer dense fiber / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / adenylate kinase / AMP kinase activity / nucleobase-containing small molecule interconversion / nucleoside-diphosphate kinase / Interconversion of nucleotide di- and triphosphates / nucleoside diphosphate kinase activity / ATP metabolic process / extracellular exosome / ATP binding / cytoplasm / cytosol
Similarity search - Function
Adenylate kinase isoenzyme 1 / Adenylate kinase, isozyme 1/5 / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / Adenylate kinase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Adenylate kinase isoenzyme 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsYu, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of human adenylate kinase 1 mutant-R97W.
Authors: Yu, J.
History
DepositionNov 7, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenylate kinase isoenzyme 1


Theoretical massNumber of molelcules
Total (without water)21,6971
Polymers21,6971
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 300structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Adenylate kinase isoenzyme 1


Mass: 21696.891 Da / Num. of mol.: 1 / Mutation: R97W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AK1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00568
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
123isotropic12D 1H-13C HSQC
132isotropic13D HN(CA)CB
142isotropic13D CBCA(CO)NH
152isotropic13D HNCA
1122isotropic13D HN(CO)CA
1112isotropic13D HNCO
1102isotropic13D HN(CA)CO
192isotropic13D H(CCO)NH
182isotropic13D CC(CO)NH
172isotropic13D HBHA(CO)NH
163isotropic13D (H)CCH-TOCSY
1163isotropic13D CCH-TOCSY
1152isotropic13D 15N-edited NOESY-HSQC
1143isotropic13D 13C-edited NOESY-HSQC
1133isotropic1(HB)CB(CGCD)HD
1173isotropic1(HB)CB(CGCDCE)HE

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.88 mM [U-99% 15N] 15N_R97W, 90% H2O/10% D2O0.88 mM [U-99% 15N] R97W, 10 mM MOPS, 50 mM NaCl, 100 mM Na2SO4, 5 mM EDTA15N_R97W90% H2O/10% D2O
solution20.88 mM [U-99% 13C; U-99% 15N] 15N_13C_R97W10% D2O, 90% H2O/10% D2O0.88 mM [U-99% 13C; U-99% 15N] R97W, 10 mM MOPS, 50 mM NaCl, 100 mM Na2SO4, 5 mM EDTA15N_13C_R97W10% D2O90% H2O/10% D2O
solution30.88 mM [U-99% 13C; U-99% 15N] 15N_13C_R97W99% D2O, 99% D2O0.88 mM [U-99% 13C; U-99% 15N] R97W, 10 mM MOPS, 50 mM NaCl, 100 mM Na2SO4, 5 mM EDTA15N_13C_R97W99% D2O99% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.88 mM15N_R97W[U-99% 15N]1
0.88 mM15N_13C_R97W10% D2O[U-99% 13C; U-99% 15N]2
0.88 mM15N_13C_R97W99% D2O[U-99% 13C; U-99% 15N]3
Sample conditionsIonic strength: 160 mM / Label: MOPS / pH: 6.2 / 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
NameVersionDeveloperClassification
NMRFAM-SPARKYLee W., Tonelli M., Markley J. L.chemical shift assignment
ARIA2alphaCNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
ARIA2alphaCNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 20

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