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- PDB-8rj9: E. coli adenylate kinase Asp84Ala variant in complex with two ADP... -

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Basic information

Entry
Database: PDB / ID: 8rj9
TitleE. coli adenylate kinase Asp84Ala variant in complex with two ADP molecules as a result of enzymatic AP4A hydrolysis.
ComponentsAdenylate kinase
KeywordsTRANSFERASE / ATP:AMP PHOSPHOTRANSFERASE / ENERGY METABOLISM / AP4A HYDROLYSIS / POTENTIAL MOONLIGHTING PROTEIN
Function / homology
Function and homology information


purine ribonucleotide interconversion / ADP biosynthetic process / nucleoside monophosphate metabolic process / nucleoside diphosphate metabolic process / adenylate kinase / adenylate kinase activity / AMP salvage / nucleoside diphosphate kinase activity / AMP binding / magnesium ion binding ...purine ribonucleotide interconversion / ADP biosynthetic process / nucleoside monophosphate metabolic process / nucleoside diphosphate metabolic process / adenylate kinase / adenylate kinase activity / AMP salvage / nucleoside diphosphate kinase activity / AMP binding / magnesium ion binding / ATP binding / cytoplasm / cytosol
Similarity search - Function
Adenylate kinase, active site lid domain / Adenylate kinase, active site lid / Adenylate kinase subfamily / Adenylate kinase / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Adenylate kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsTischlik, S. / Ronge, P. / Wolf-Watz, M. / Sauer-Eriksson, A.E.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Citation
Journal: Sci Adv / Year: 2024
Title: Magnesium Induced Structural Preorganization in the Active Site of Adenylate Kinase.
Authors: Abdul Raafik, A.T. / Tischlik, S. / Nagy, T.M. / Phoeurk, C. / Schierholtz, L. / Aden, J. / Rogne, P. / Drescher, M. / Nam, K. / Sauer-Eriksson, A.E. / Wolf-Watz, M.
#1: Journal: Biochemistry / Year: 2023
Title: Insights into Enzymatic Catalysis from Binding and Hydrolysis of Diadenosine Tetraphosphate by
Authors: Tischlik, S. / Oelker, M. / Rogne, P. / Sauer-Eriksson, A.E. / Drescher, M. / Wolf-Watz, M.
History
DepositionDec 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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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)48,8616
Polymers47,1522
Non-polymers1,7094
Water9,386521
1
A: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4303
Polymers23,5761
Non-polymers8542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4303
Polymers23,5761
Non-polymers8542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.776, 72.609, 78.111
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Adenylate kinase / AK / ATP-AMP transphosphorylase / ATP:AMP phosphotransferase / Adenylate monophosphate kinase


Mass: 23576.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: adk, dnaW, plsA, b0474, JW0463 / Production host: Escherichia coli (E. coli) / References: UniProt: P69441, adenylate kinase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 521 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 24-26% PEG3350, 100 mM Bis-Tris propane. / PH range: 6.4-7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.59→44.42 Å / Num. obs: 61752 / % possible obs: 99.1 % / Redundancy: 8.5 % / Biso Wilson estimate: 22.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.049 / Net I/σ(I): 12.1
Reflection shellResolution: 1.59→1.65 Å / Rmerge(I) obs: 1.817 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 6030 / CC1/2: 0.462 / Rpim(I) all: 0.989

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→44.42 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2029 2002 3.24 %
Rwork0.1501 --
obs0.1519 61729 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.59→44.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3306 0 108 521 3935
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093627
X-RAY DIFFRACTIONf_angle_d1.1984937
X-RAY DIFFRACTIONf_dihedral_angle_d18.5761419
X-RAY DIFFRACTIONf_chiral_restr0.054549
X-RAY DIFFRACTIONf_plane_restr0.006639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.630.35711430.29314162X-RAY DIFFRACTION98
1.63-1.670.30971360.25454172X-RAY DIFFRACTION98
1.67-1.720.28561440.22794169X-RAY DIFFRACTION98
1.72-1.780.29591350.21134222X-RAY DIFFRACTION98
1.78-1.840.25811430.19594193X-RAY DIFFRACTION99
1.84-1.920.23511390.17544203X-RAY DIFFRACTION98
1.92-20.261400.15824241X-RAY DIFFRACTION99
2-2.110.17831410.14384225X-RAY DIFFRACTION99
2.11-2.240.20371360.13044284X-RAY DIFFRACTION99
2.24-2.410.19421510.13034271X-RAY DIFFRACTION99
2.41-2.660.17751440.13574296X-RAY DIFFRACTION100
2.66-3.040.19031420.14344353X-RAY DIFFRACTION100
3.04-3.830.18661500.13244380X-RAY DIFFRACTION100
3.83-44.420.18331580.14374556X-RAY DIFFRACTION100

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