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- PDB-3aky: STABILITY, ACTIVITY AND STRUCTURE OF ADENYLATE KINASE MUTANTS -

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Basic information

Entry
Database: PDB / ID: 3aky
TitleSTABILITY, ACTIVITY AND STRUCTURE OF ADENYLATE KINASE MUTANTS
ComponentsADENYLATE KINASE
KeywordsADENYLATE KINASE / ATP:AMP PHOSPHOTRANSFERASE / MYOKINASE
Function / homology
Function and homology information


pre-replicative complex assembly / AMP metabolic process / Interconversion of nucleotide di- and triphosphates / ADP biosynthetic process / adenylate kinase / AMP kinase activity / nucleotide metabolic process / AMP binding / DNA replication origin binding / DNA replication initiation ...pre-replicative complex assembly / AMP metabolic process / Interconversion of nucleotide di- and triphosphates / ADP biosynthetic process / adenylate kinase / AMP kinase activity / nucleotide metabolic process / AMP binding / DNA replication origin binding / DNA replication initiation / ATP metabolic process / mitochondrial intermembrane space / mitochondrion / ATP binding / cytoplasm / cytosol
Similarity search - Function
Adenylate kinase 2 / Adenylate kinase, active site lid domain / Adenylate kinase, active site lid / Adenylate kinase subfamily / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / Adenylate kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold ...Adenylate kinase 2 / Adenylate kinase, active site lid domain / Adenylate kinase, active site lid / Adenylate kinase subfamily / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / Adenylate kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BIS(ADENOSINE)-5'-PENTAPHOSPHATE / IMIDAZOLE / Adenylate kinase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.23 Å
AuthorsAbele, U. / Schulz, G.E.
Citation
Journal: Eur.J.Biochem. / Year: 1995
Title: Stability, activity and structure of adenylate kinase mutants.
Authors: Spuergin, P. / Abele, U. / Schulz, G.E.
#1: Journal: Protein Sci. / Year: 1995
Title: High-Resolution Structures of Adenylate Kinase from Yeast Ligated with Inhibitor Ap5A, Showing the Pathway of Phosphoryl Transfer
Authors: Abele, U. / Schulz, G.E.
#2: Journal: Nucleic Acids Res. / Year: 1987
Title: The C-DNA Sequence Encoding Cytosolic Adenylate Kinase from Baker'S Yeast (Saccharomyces Cerevisiae)
Authors: Proba, K. / Tomasselli, A.G. / Nielsen, P. / Schulz, G.E.
#3: Journal: J.Mol.Biol. / Year: 1987
Title: Structure of the Complex of Yeast Adenylate Kinase with the Inhibitor Ap5A at 2.6 Angstroms Resolution
Authors: Egner, U. / Tomasselli, A.G. / Schulz, G.E.
#4: Journal: Eur.J.Biochem. / Year: 1986
Title: The Complete Amino Acid Sequence of Adenylate Kinase from Baker'S Yeast
Authors: Tomasselli, A.G. / Mast, E. / Janes, W. / Schiltz, E.
History
DepositionJul 28, 1995Processing site: BNL
Revision 1.0Nov 14, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 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: ADENYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0883
Polymers24,1031
Non-polymers9852
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.000, 40.400, 45.300
Angle α, β, γ (deg.)111.70, 109.00, 63.30
Int Tables number1
Space group name H-MP1
Atom site foot note1: CIS PROLINE - PRO 92

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Components

#1: Protein ADENYLATE KINASE / ATP\:AMP PHOSPHOTRANSFERASE / MYOKINASE


Mass: 24102.533 Da / Num. of mol.: 1 / Mutation: I213F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PUAKY / Production host: Escherichia coli (E. coli) / References: UniProt: P07170, adenylate kinase
#2: Chemical ChemComp-AP5 / BIS(ADENOSINE)-5'-PENTAPHOSPHATE


Mass: 916.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H29N10O22P5
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.22 Å3/Da / Density % sol: 44.67 %
Crystal
*PLUS
Density % sol: 46 %
Crystal grow
*PLUS
pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlprotein 1drop
21.6 mMAp5A1drop
326 %PEG80001drop
460 mMimidazole/HCl1drop
529 %PEG80001reservoir
660 mMimidazole/HCl1reservoir
70.5 %2-mercaptoethanol1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: 1990
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.23 Å / Num. obs: 10242 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.041
Reflection
*PLUS
Lowest resolution: 9999 Å / Rmerge(I) obs: 0.041

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.23→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.149 --
obs0.149 9427 94.4 %
Displacement parametersBiso mean: 31 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 2.23→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2058 0 72 378 2508
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.46
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it3.5
X-RAY DIFFRACTIONx_scangle_it5
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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