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- PDB-7de3: Human adenylate kinase 1 (hAK1) mutant-R128W -

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Basic information

Entry
Database: PDB / ID: 7de3
TitleHuman adenylate kinase 1 (hAK1) mutant-R128W
ComponentsAdenylate kinase isoenzyme 1
KeywordsTRANSFERASE / cellular energy homeostasis / adenine nucleotide metabolism / CELL CYCLE
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 / cytosol / cytoplasm
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.197 Å
AuthorsLin, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of human adenylate kinase 1 mutant-R128W.
Authors: Lin, W.
History
DepositionNov 1, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

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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
Water3,063170
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10390 Å2
Unit cell
Length a, b, c (Å)95.167, 95.167, 47.961
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-339-

HOH

21A-350-

HOH

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Components

#1: Protein Adenylate kinase isoenzyme 1 / AK 1 / ATP-AMP transphosphorylase 1 / ATP:AMP phosphotransferase / Adenylate monophosphate kinase / Myokinase


Mass: 21696.891 Da / Num. of mol.: 1 / Mutation: R128W
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, adenylate kinase, nucleoside-diphosphate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG 3350,0.2M Ammonium acetate / PH range: 6.6-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jun 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.197→33.647 Å / Num. obs: 11451 / % possible obs: 97.69 % / Redundancy: 13.5 % / CC1/2: 0.938 / Net I/σ(I): 17
Reflection shellResolution: 2.197→2.275 Å / Rmerge(I) obs: 0.154 / Num. unique obs: 22139

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Processing

Software
NameVersionClassification
PHENIX1.16-3549refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3adk

3adk


Resolution: 2.197→33.647 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2595 --
Rwork0.205 --
obs-11451 97.69 %
Displacement parametersBiso max: 89.08 Å2 / Biso mean: 32.0887 Å2 / Biso min: 9.39 Å2
Refinement stepCycle: LAST / Resolution: 2.197→33.647 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1455 0 0 170 1625

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