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- PDB-2ak3: THE THREE-DIMENSIONAL STRUCTURE OF THE COMPLEX BETWEEN MITOCHONDR... -

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Basic information

Entry
Database: PDB / ID: 2ak3
TitleTHE THREE-DIMENSIONAL STRUCTURE OF THE COMPLEX BETWEEN MITOCHONDRIAL MATRIX ADENYLATE KINASE AND ITS SUBSTRATE AMP AT 1.85 ANGSTROMS RESOLUTION
ComponentsADENYLATE KINASE ISOENZYME-3
KeywordsTRANSFERASE (PHOSPHOTRANSFERASE)
Function / homology
Function and homology information


nucleoside-triphosphate-adenylate kinase / ITP metabolic process / UTP metabolic process / nucleoside triphosphate adenylate kinase activity / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / Factors involved in megakaryocyte development and platelet production / AMP kinase activity / GTP metabolic process ...nucleoside-triphosphate-adenylate kinase / ITP metabolic process / UTP metabolic process / nucleoside triphosphate adenylate kinase activity / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / Factors involved in megakaryocyte development and platelet production / AMP kinase activity / GTP metabolic process / mitochondrial matrix / GTP binding / mitochondrion / ATP binding / cytoplasm
Similarity search - Function
Adenylate kinase 3/4, mitochondrial / Adenylate kinase, active site lid domain superfamily / 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 ...Adenylate kinase 3/4, mitochondrial / Adenylate kinase, active site lid domain superfamily / 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
ADENOSINE MONOPHOSPHATE / GTP:AMP phosphotransferase AK3, mitochondrial
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.85 Å
AuthorsDiederichs, K. / Schulz, G.E.
Citation
Journal: J.Mol.Biol. / Year: 1991
Title: The refined structure of the complex between adenylate kinase from beef heart mitochondrial matrix and its substrate AMP at 1.85 A resolution.
Authors: Diederichs, K. / Schulz, G.E.
#1: Journal: Biochemistry / Year: 1990
Title: The Three-Dimensional Structure of the Complex between Mitochondrial Matrix Adenylate Kinase and its Substrate AMP
Authors: Diederichs, K. / Schulz, G.E.
#2: Journal: J.Mol.Biol. / Year: 1990
Title: Induced-Fit Movements in Adenylate Kinase
Authors: Schulz, G.E. / Muller, C.W. / Diederichs, K.
#3: Journal: J.Biol.Chem. / Year: 1989
Title: Cloning and Characterization of Cdna for Mitochondrial GTP:AMP Phosphotransferase of Bovine Liver
Authors: Yamada, M. / Shahjahan, M. / Tanabe, T. / Kishi, F. / Nakazawa, A.
#4: Journal: FEBS Lett. / Year: 1986
Title: The Complete Primary Structure of GTP:AMP Phosphotransferase from Beef Heart Mitochondria
Authors: Tomasselli, A.G. / Frank, R. / Schiltz, E.
#5: Journal: Eur.J.Biochem. / Year: 1984
Title: The Amino Acid Sequence of GTP:AMP Phosphotransferase from Beef-Heart Mitochondria: Extensive Homology with Cytosolic Adenylate Kinase
Authors: Wieland, B. / Tomasselli, A.G. / Noda, L.H. / Frank, R. / Schulz, G.E.
#6: Journal: Eur.J.Biochem. / Year: 1979
Title: Mitochondrial GTP-AMP Phosphotransferase: 1. Purification and Properties
Authors: Tomasselli, A.G. / Schirmer, R.H. / Noda, L.H.
#7: Journal: Eur.J.Biochem. / Year: 1979
Title: Mitochondrial GTP-AMP Phosphotransferase: 2. Kinetic and Equilibrium Dialysis Studies
Authors: Tomasselli, A.G. / Noda, L.H.
History
DepositionMar 7, 1995Processing site: BNL
SupersessionMay 8, 1995ID: 1AK3
Revision 1.0May 8, 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 / 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_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-3
B: ADENYLATE KINASE ISOENZYME-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0376
Polymers51,1512
Non-polymers8874
Water6,864381
1
A: ADENYLATE KINASE ISOENZYME-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0193
Polymers25,5751
Non-polymers4432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADENYLATE KINASE ISOENZYME-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0193
Polymers25,5751
Non-polymers4432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.830, 66.990, 155.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.985, 0.031, 0.171), (-0.002, 0.985, -0.171), (-0.174, 0.168, 0.97)
Vector: 27.25, 10.96, -45)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX CHAIN RESIDUES CHAIN RESIDUES RMSD M1 A 0 - A 219 B 0 - B 219 1.508

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Components

#1: Protein ADENYLATE KINASE ISOENZYME-3


Mass: 25575.268 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle)
References: UniProt: P08760, nucleoside-triphosphate-adenylate kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.46 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlenzyme1drop
275 mMMOPS1drop
31 mMEDTA1drop
40.1 %1dropNaN3
53 mMAMP1drop
612 %(w/v)PEG80001drop
716 %(w/v)PEG80001reservoir
875 mMMOPS1reservoir

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Data collection

ReflectionHighest resolution: 1.85 Å / Num. obs: 42879 / % possible obs: 94.5 %
Reflection
*PLUS
Lowest resolution: 9999 Å / Observed criterion σ(I): 0

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.85→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.189 --
obs0.189 42519 94.4 %
Refinement stepCycle: LAST / Resolution: 1.85→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3560 0 56 381 3997
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg3.2
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_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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