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- PDB-1dvr: STRUCTURE OF A MUTANT ADENYLATE KINASE LIGATED WITH AN ATP-ANALOG... -

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Basic information

Entry
Database: PDB / ID: 1dvr
TitleSTRUCTURE OF A MUTANT ADENYLATE KINASE LIGATED WITH AN ATP-ANALOGUE SHOWING DOMAIN CLOSURE OVER ATP
ComponentsADENYLATE KINASE
KeywordsTRANSFERASE (PHOSPHOTRANSFERASE) / NUCLEOSIDE MONOPHOSPHATE KINASE / MYOKINASE
Function / homology
Function and homology information


pre-replicative complex assembly / AMP metabolic process / Interconversion of nucleotide di- and triphosphates / ADP biosynthetic process / adenylate kinase / AMP kinase activity / nucleotide metabolic process / AMP binding / DNA replication origin binding / DNA replication initiation ...pre-replicative complex assembly / AMP metabolic process / Interconversion of nucleotide di- and triphosphates / ADP biosynthetic process / adenylate kinase / AMP kinase activity / nucleotide metabolic process / AMP binding / DNA replication origin binding / DNA replication initiation / ATP metabolic process / mitochondrial intermembrane space / mitochondrion / ATP binding / cytosol / 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
Chem-ATF / Adenylate kinase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.36 Å
AuthorsSchlauderer, G.J. / Schulz, G.E.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Structure of a mutant adenylate kinase ligated with an ATP-analogue showing domain closure over ATP.
Authors: Schlauderer, G.J. / Proba, K. / Schulz, G.E.
#1: Journal: Eur.J.Biochem. / Year: 1995
Title: Stability, Activity and Structure of Adenylate Kinase Mutants
Authors: Spuergin, P. / Abele, U. / Schulz, G.E.
#2: Journal: Protein Sci. / Year: 1995
Title: High-Resolution Structures of Adenylate Kinase from Yeast Ligated with Inhibitor Ap5A, Showing the Pathway of Phosphoryl Transfer
Authors: Abele, U. / Schulz, G.E.
#3: 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.
#4: Journal: Nucleic Acids Res. / Year: 1987
Title: The C-DNA Sequence Encoding Cytosolic Adenylate Kinase from Baker'S Yeast (Saccharomyces Cerevisiae)
Authors: Proba, K. / Tomasselli, A.G. / Nielsen, P. / Schulz, G.E.
#5: Journal: J.Mol.Biol. / Year: 1987
Title: Structure of the Complex of Yeast Adenylate Kinase with the Inhibitor Ap5A at 2.6 Angstroms Resolution
Authors: Egner, U. / Tomasselli, A.G. / Schulz, G.E.
#6: Journal: Eur.J.Biochem. / Year: 1986
Title: The Complete Amino Acid Sequence of Adenylate Kinase from Baker'S Yeast
Authors: Tomasselli, A.G. / Mast, E. / Janes, W. / Schiltz, E.
History
DepositionDec 14, 1995Processing site: BNL
Revision 1.0Apr 3, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Advisory / Data collection / Other
Category: diffrn_source / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _diffrn_source.type / _pdbx_database_status.process_site
Revision 1.4Nov 3, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 700SHEET THE HELIX AND SHEET ASSIGNMENTS BELOW ARE AUTOMATIC WITH PROGRAM DSSP.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADENYLATE KINASE
B: ADENYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0994
Polymers48,0172
Non-polymers1,0822
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.800, 73.400, 118.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO A 92 / 2: CIS PROLINE - PRO B 92
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.489945, -0.809503, -0.323511), (-0.812717, 0.289904, 0.505417), (-0.315349, 0.510549, -0.799934)
Vector: 65.3682, 45.295, -12.509)

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Components

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


Mass: 24008.525 Da / Num. of mol.: 2 / Mutation: D89V, R165I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Cellular location: CYTOSOL / Plasmid: PUAKYI / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: P07170, adenylate kinase
#2: Chemical ChemComp-ATF / PHOSPHODIFLUOROMETHYLPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 541.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H16F2N5O12P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.17 Å3/Da / Density % sol: 43.29 %
Crystal
*PLUS
Density % sol: 43 %
Crystal grow
*PLUS
pH: 6.3 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.4 mMenzyme1drop
22.5 mMAMPPCF2P1drop
350 mMimidazole1drop
475 mM1dropKCl
50.05 %octyl-beta-glucoside1drop
621 %PEG33501drop
750 mMimidazole1reservoir
828 %PEG33501reservoir

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: 1991
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.36→10 Å / Num. obs: 15793 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.058
Reflection
*PLUS
Rmerge(I) obs: 0.058

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.36→10 Å / σ(F): 0
Details: RESIDUES SER 166 - ASN 169 IN CHAIN HAVE WEAK DENSITY.
RfactorNum. reflection% reflection
Rwork0.191 --
obs0.191 15793 90 %
Displacement parametersBiso mean: 29 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.36→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3366 0 66 161 3593
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.7
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_it2.41.5
X-RAY DIFFRACTIONx_mcangle_it3.92
X-RAY DIFFRACTIONx_scbond_it6.42
X-RAY DIFFRACTIONx_scangle_it8.72.5
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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