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- PDB-2aky: HIGH-RESOLUTION STRUCTURES OF ADENYLATE KINASE FROM YEAST LIGATED... -

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Basic information

Entry
Database: PDB / ID: 2aky
TitleHIGH-RESOLUTION STRUCTURES OF ADENYLATE KINASE FROM YEAST LIGATED WITH INHIBITOR AP5A, SHOWING THE PATHWAY OF PHOSPHORYL TRANSFER
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 / Adenylate kinase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 1.96 Å
AuthorsAbele, U. / Schulz, G.E.
Citation
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.
#1: Journal: Eur.J.Biochem. / Year: 1995
Title: Stability, Activity and Structure of Adenylate Kinase Mutants
Authors: Spuergin, P. / 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 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)25,0093
Polymers24,0691
Non-polymers9412
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.000, 40.400, 45.500
Angle α, β, γ (deg.)110.70, 108.80, 64.70
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: 24068.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: RED STAR, MILWAUKEE / Cellular location: CYTOSOL / Production host: Escherichia coli (E. coli) / References: UniProt: P07170, adenylate kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-AP5 / BIS(ADENOSINE)-5'-PENTAPHOSPHATE


Mass: 916.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H29N10O22P5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.27 Å3/Da / Density % sol: 45.9 %
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/mlprotein1drop
21.1 mMAp5A1drop
326 %PEG80001drop
460 mMIm1drop
530 %PEG80001reservoir
660 mMIm1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: 1988
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.96 Å / Num. obs: 15638 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 1.5 %
Reflection
*PLUS
Lowest resolution: 9999 Å

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
SYNDUCdata reduction
X-PLOR3.1phasing
RefinementResolution: 1.96→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.176 --
obs0.176 15477 99.2 %
Displacement parametersBiso mean: 32 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.96→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2055 0 66 459 2580
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_deg1.4
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

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