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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 / homologyAdenylate kinase / Adenylate kinase, active site lid domain / Interconversion of nucleotide di- and triphosphates / Adenylate kinase signature. / Adenylate kinase, active site lid / Adenylate kinase, conserved site / Adenylate kinase 2 / P-loop containing nucleoside triphosphate hydrolase / Adenylate kinase subfamily / Adenylate kinase/UMP-CMP kinase ...Adenylate kinase / Adenylate kinase, active site lid domain / Interconversion of nucleotide di- and triphosphates / Adenylate kinase signature. / Adenylate kinase, active site lid / Adenylate kinase, conserved site / Adenylate kinase 2 / P-loop containing nucleoside triphosphate hydrolase / Adenylate kinase subfamily / Adenylate kinase/UMP-CMP kinase / sperm mitochondrial sheath / ADP biosynthetic process / adenylate kinase / adenylate kinase activity / mitochondrial intermembrane space / mitochondrial inner membrane / mitochondrion / ATP binding / Adenylate kinase 2, mitochondrial
Function and homology information
Specimen sourceBos taurus (cattle)
MethodX-RAY DIFFRACTION / 1.92 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 29, 1995 / Release: Jun 10, 1996
RevisionDateData content typeGroupProviderType
1.0Jun 10, 1996Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADENYLATE KINASE ISOENZYME-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6372
Polyers25,5411
Non-polymers961
Water2,108117
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
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-MP 21 21 21

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Components

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


Mass: 25540.504 Da / Num. of mol.: 1 / Details: PRECIPITANT POLYETHYLENE GLYCOL / Source: (natural) Bos taurus (cattle) / Genus: Bos / 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 / Formula: SO4 / Sulfate
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Formula: H2O / Water
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.

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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 / Density percent sol: 54 %
Crystal grow
*PLUS
Method: unknown
components of the solutions
*PLUS
Common name: PEG / Details: precipitant

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Data collection

SourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Collection date: 1992
RadiationMonochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionD resolution high: 1.92 Å / D resolution low: 1 Å / Number obs: 20850 / Observed criterion sigma I: 0 / Rmerge I obs: 0.077 / Redundancy: 13 % / Percent possible obs: 98

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Processing

Software
NameVersionClassification
XDSdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefineSigma F: 0
Displacement parametersB iso mean: 34 Å2
Least-squares processR factor R work: 0.222 / R factor obs: 0.222 / Highest resolution: 1.92 Å / Lowest resolution: 1 Å / Number reflection obs: 20850 / Percent reflection obs: 98
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refine hist #LASTHighest resolution: 1.92 Å / Lowest resolution: 1 Å
Number of atoms included #LASTProtein: 1699 / Nucleic acid: 0 / Ligand: 5 / Solvent: 117 / Total: 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_it2.42.0
X-RAY DIFFRACTIONx_scbond_it3.73.5
X-RAY DIFFRACTIONx_scangle_it5.45.0
Software
*PLUS
Name: X-PLOR / Classification: refinement

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