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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
DescriptorADENYLATE KINASE ISOENZYME-2
KeywordsPHOSPHOTRANSFERASE / NUCLEOSIDE MONOPHOSPHATE KINASE
Specimen sourceBos taurus / mammal / cattle / ウシ /
MethodX-ray diffraction (1.92 Å resolution)
AuthorsSchlauderer, G.J. / Schulz, G.E.
CitationProtein Sci., 1996, 5, 434-441

primary. Protein Sci., 1996, 5, 434-441 Yorodumi Papers
The structure of bovine mitochondrial adenylate kinase: comparison with isoenzymes in other compartments.
Schlauderer, G.J. / Schulz, G.E.

#1. Structure, 1995, 3, 483-
Movie of the Structural Changes During a Catalytic Cycle of Nucleoside Monophosphate Kinases
Vonrhein, C. / Schlauderer, G.J. / Schulz, G.E.

#2. J.Biol.Chem., 1987, 262, 11785-
Isolation and Characterization of Two Types of Cdna for Mitochondrial Adenylate Kinase and Their Expression in Escherichia Coli
Kishi, F. / Tanizawa, Y. / Nakazawa, A.

#3. Eur.J.Biochem., 1986, 154, 205-
Mitochondrial Adenylate Kinase (Ak2) from Bovine Heart. The Complete Primary Structure
Frank, R. / Trosin, M. / Tomasselli, A.G. / Noda, L. / Krauth-Siegel, R.L. / Schirmer, R.H.

#4. Eur.J.Biochem., 1980, 103, 481-
Mitochondrial ATP:AMP Phosphotransferase from Beef Heart: Purification and Properties
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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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: Polypeptide(L)ADENYLATE KINASE ISOENZYME-2 / ATP\:AMP PHOSPHOTRANSFERASE / MYOKINASE


Mass: 25540.504 Da / Num. of mol.: 1 / Details: PRECIPITANT POLYETHYLENE GLYCOL / Source: (natural) Bos taurus / mammal / ウシ / / References: UniProt: P08166, EC: 2.7.4.3

Cellular component

Molecular function

Biological process

#2: ChemicalChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Formula: SO4
#3: WaterChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Formula: H2O
Compound detailsTHE 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
Temp unit: unknown / Method: unknown
Crystal grow comp
*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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