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- PDB-3adk: REFINED STRUCTURE OF PORCINE CYTOSOLIC ADENYLATE KINASE AT 2.1 AN... -

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Basic information

Entry
Database: PDB / ID: 3adk
TitleREFINED STRUCTURE OF PORCINE CYTOSOLIC ADENYLATE KINASE AT 2.1 ANGSTROMS RESOLUTION
ComponentsADENYLATE KINASE
KeywordsTRANSFERASE(PHOSPHOTRANSFERASE)
Function / homology
Function and homology information


Interconversion of nucleotide di- and triphosphates / nucleoside-phosphate kinase / dAMP kinase activity / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / adenylate kinase / AMP kinase activity / nucleoside-diphosphate kinase / nucleoside diphosphate kinase activity ...Interconversion of nucleotide di- and triphosphates / nucleoside-phosphate kinase / dAMP kinase activity / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / adenylate kinase / AMP kinase activity / nucleoside-diphosphate kinase / nucleoside diphosphate kinase activity / ATP metabolic process / ATP binding / cytoplasm
Similarity search - Function
Adenylate kinase isoenzyme 1 / Adenylate kinase, isozyme 1/5 / 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 isoenzyme 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsSchulz, G.E.
Citation
Journal: J.Mol.Biol. / Year: 1988
Title: Refined structure of porcine cytosolic adenylate kinase at 2.1 A resolution.
Authors: Dreusicke, D. / Karplus, P.A. / Schulz, G.E.
#1: Journal: Eur.J.Biochem. / Year: 1986
Title: Structural Relationships in the Adenylate Kinase Family
Authors: Schulz, G.E. / Schiltz, E. / Tomasselli, A.G. / Frank, R. / Brune, M. / Wittinghofer, A. / Schirmer, R.H.
#2: Journal: FEBS Lett. / Year: 1986
Title: The Glycine-Rich Loop of Adenylate Kinase Forms a Giant Anion Hole
Authors: Dreusicke, D. / Schulz, G.E.
#3: Journal: J.Mol.Biol. / Year: 1977
Title: Two Conformations of Crystalline Adenylate Kinase
Authors: Sachsenheimer, W. / Schulz, G.E.
#4: Journal: J.Mol.Biol. / Year: 1977
Title: Substrate Positions and Induced-Fit in Crystalline Adenylate Kinase
Authors: Pai, E.F. / Sachsenheimer, W. / Schirmer, R.H. / Schulz, G.E.
#5: Journal: Nature / Year: 1974
Title: Three-Dimensional Structure of Adenylate Kinase
Authors: Schulz, G.E. / Elzinga, M. / Marx, F. / Schirmer, R.H.
#6: Journal: Nature / Year: 1974
Title: Topological Comparison of Adenylate Kinase with Other Proteins
Authors: Schulz, G.E. / Schirmer, R.H.
#7: Journal: Nature / Year: 1974
Title: Comparison of Predicted and Experimentally Determined Secondary Structure of Adenylate Kinase
Authors: Schulz, G.E. / Barry, C.D. / Friedman, J. / Chou, P.Y. / Fasman, G.D. / Finkelstein, A.V. / Lim, V.I. / Ptitsyn, O.B. / Kabat, E.A. / Wu, T.T. / Levitt, M. / Robson, B. / Nagano, K.
#8: Journal: Eur.J.Biochem. / Year: 1974
Title: The Amino-Acid Sequence of Porcine Adenylate Kinase from Skeletal Muscle
Authors: Heil, A. / Mueller, G. / Noda, L. / Pinder, T. / Schirmer, H. / Schirmer, I. / Vonzabern, I.
#9: Journal: J.Mol.Biol. / Year: 1973
Title: Low Resolution Structure of Adenylate Kinase
Authors: Schulz, G.E. / Biedermann, K. / Kabsch, W. / Schirmer, R.H.
#10: Journal: Atlas of Protein Sequence and Structure,Supplement 2
Year: 1976
History
DepositionNov 19, 1987Processing site: BNL
SupersessionJan 16, 1988ID: 2ADK
Revision 1.0Jan 16, 1988Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 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_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 / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700SHEET SPECIFICATION OF THE HELICES AND SHEET STRANDS IS PROVIDED IN THE PUBLICATION CITED ON THE ...SHEET SPECIFICATION OF THE HELICES AND SHEET STRANDS IS PROVIDED IN THE PUBLICATION CITED ON THE *JRNL* RECORDS ABOVE.

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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)21,8913
Polymers21,6991
Non-polymers1922
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.500, 48.500, 141.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Atom site foot note1: RESIDUE 96 IS A CIS PROLINE.

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Components

#1: Protein ADENYLATE KINASE


Mass: 21699.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P00571, adenylate kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
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: 2.21 Å3/Da / Density % sol: 44.23 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.9 / Method: unknown / Details: Schulz, G.E., (1973) J.Mol.Biol., 80, 857.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MTris-maleate11
22.4 Mammonium sulfate11
30.7 mMprotein12

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Data collection

Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 9999 Å / Num. obs: 11518

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.1→10 Å / Rfactor Rwork: 0.193
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1519 0 10 0 1529
Refinement
*PLUS
Num. reflection obs: 10962
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.026
X-RAY DIFFRACTIONo_angle_deg3.3

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