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- PDB-1ak2: ADENYLATE KINASE ISOENZYME-2 -

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Basic information

Entry
Database: PDB / ID: 1ak2
TitleADENYLATE KINASE ISOENZYME-2
ComponentsADENYLATE KINASE ISOENZYME-2
KeywordsPHOSPHOTRANSFERASE / NUCLEOSIDE MONOPHOSPHATE KINASE
Function / homology
Function and homology information


Interconversion of nucleotide di- and triphosphates / AMP metabolic process / ADP biosynthetic process / adenylate kinase / adenylate kinase activity / sperm mitochondrial sheath / ATP metabolic process / mitochondrial intermembrane space / mitochondrial inner membrane / mitochondrion ...Interconversion of nucleotide di- and triphosphates / AMP metabolic process / ADP biosynthetic process / adenylate kinase / adenylate kinase activity / sperm mitochondrial sheath / ATP metabolic process / mitochondrial intermembrane space / mitochondrial inner membrane / mitochondrion / ATP binding / cytoplasm
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
Adenylate kinase 2, mitochondrial
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.92 Å
AuthorsSchlauderer, G.J. / Schulz, G.E.
Citation
Journal: Protein Sci. / Year: 1996
Title: The structure of bovine mitochondrial adenylate kinase: comparison with isoenzymes in other compartments.
Authors: Schlauderer, G.J. / Schulz, G.E.
#1: Journal: Structure / Year: 1995
Title: Movie of the Structural Changes During a Catalytic Cycle of Nucleoside Monophosphate Kinases
Authors: Vonrhein, C. / Schlauderer, G.J. / Schulz, G.E.
#2: Journal: J.Biol.Chem. / Year: 1987
Title: Isolation and Characterization of Two Types of Cdna for Mitochondrial Adenylate Kinase and Their Expression in Escherichia Coli
Authors: Kishi, F. / Tanizawa, Y. / Nakazawa, A.
#3: Journal: Eur.J.Biochem. / Year: 1986
Title: Mitochondrial Adenylate Kinase (Ak2) from Bovine Heart. The Complete Primary Structure
Authors: Frank, R. / Trosin, M. / Tomasselli, A.G. / Noda, L. / Krauth-Siegel, R.L. / Schirmer, R.H.
#4: Journal: Eur.J.Biochem. / Year: 1980
Title: Mitochondrial ATP:AMP Phosphotransferase from Beef Heart: Purification and Properties
Authors: Tomasselli, A.G. / Noda, L.H.
History
DepositionDec 29, 1995Processing site: BNL
Revision 1.0Jun 10, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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

Downloads & links

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Assembly

Deposited unit
A: ADENYLATE KINASE ISOENZYME-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6372
Polymers25,5411
Non-polymers961
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.200, 50.100, 122.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ADENYLATE KINASE ISOENZYME-2 / ATP\:AMP PHOSPHOTRANSFERASE / MYOKINASE


Mass: 25540.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PRECIPITANT POLYETHYLENE GLYCOL / Source: (natural) Bos taurus (cattle) / Organ: LIVER / Organelle: MITOCHONDRIA INTERMEMBRANE SPACE / References: UniProt: P08166, adenylate kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE SECONDARY STRUCTURAL ELEMENTS PRESENTED BELOW ARE FROM PROGRAM DSSP. FOR MANUAL ASSIGNMENTS ...THE SECONDARY STRUCTURAL ELEMENTS PRESENTED BELOW ARE FROM PROGRAM DSSP. FOR MANUAL ASSIGNMENTS PLEASE SEE THE PUBLICATION.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 54 %
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
Common name: PEG / Details: precipitant

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Data collection

Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.92→10 Å / Num. obs: 20850 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 13 % / Rmerge(I) obs: 0.077

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Processing

Software
NameVersionClassification
XDSdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementResolution: 1.92→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.222 --
obs0.222 20850 98 %
Displacement parametersBiso mean: 34 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 1.92→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1699 0 5 117 1821
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.6
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_it1.31.5
X-RAY DIFFRACTIONx_mcangle_it2.42
X-RAY DIFFRACTIONx_scbond_it3.73.5
X-RAY DIFFRACTIONx_scangle_it5.45
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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