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- PDB-8q2b: E. coli Adenylate Kinase variant D158A (AK D158A) showing signifi... -

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Basic information

Entry
Database: PDB / ID: 8q2b
TitleE. coli Adenylate Kinase variant D158A (AK D158A) showing significant changes to the stacking of catalytic arginine side chains
ComponentsAdenylate kinase
KeywordsTRANSFERASE / PHOSPHOTRANSFERASE / ADENYLATE KINASE / D158A VARIANT / AP5A LIGAND / PROTEIN DYNAMICS
Function / homology
Function and homology information


CDP biosynthetic process / (d)CMP kinase activity / UMP kinase activity / adenylate kinase / adenylate kinase activity / AMP salvage / UDP biosynthetic process / nucleoside diphosphate kinase activity / phosphorylation / ATP binding / 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
BIS(ADENOSINE)-5'-PENTAPHOSPHATE / Adenylate kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsSauer, U.H. / Wolf-Watz, M. / Nam, K.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2021-04513 Sweden
CitationJournal: J.Chem.Inf.Model. / Year: 2024
Title: Elucidating Dynamics of Adenylate Kinase from Enzyme Opening to Ligand Release.
Authors: Nam, K. / Arattu Thodika, A.R. / Grundstrom, C. / Sauer, U.H. / Wolf-Watz, M.
History
DepositionAug 1, 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

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Assembly

Deposited unit
A: Adenylate kinase
B: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2906
Polymers47,1522
Non-polymers2,1384
Water8,215456
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Gel filtration provided a clear peak corresponding to the AK monomer MW.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-14 kcal/mol
Surface area20870 Å2
Unit cell
Length a, b, c (Å)57.283, 77.974, 59.911
Angle α, β, γ (deg.)90.00, 93.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Adenylate kinase


Mass: 23576.020 Da / Num. of mol.: 2 / Mutation: D158A
Source method: isolated from a genetically manipulated source
Details: AK D158A variant / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: adk / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3TLA2
#2: Chemical ChemComp-AP5 / BIS(ADENOSINE)-5'-PENTAPHOSPHATE


Mass: 916.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H29N10O22P5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / 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: 2.84 Å3/Da / Density % sol: 56.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Crystallization: 2 ul of purified AK-D158A at 16.4 mg/ml, mixed with the non-hydrolysable inhibitor Ap5A at a final concentration of 5 mM and 2 ul of precipitant buffer containing 32% PEG ...Details: Crystallization: 2 ul of purified AK-D158A at 16.4 mg/ml, mixed with the non-hydrolysable inhibitor Ap5A at a final concentration of 5 mM and 2 ul of precipitant buffer containing 32% PEG 8K, 0.2 M AmSO4, 0.1 M Cacodylate at pH 6.5.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87293 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: May 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87293 Å / Relative weight: 1
ReflectionResolution: 1.76→47.45 Å / Num. obs: 52176 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 22.1 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.045 / Rrim(I) all: 0.118 / Net I/σ(I): 11.2
Reflection shellResolution: 1.76→1.82 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.097 / Mean I/σ(I) obs: 1.82 / Num. unique obs: 5114 / CC1/2: 0.627 / Rpim(I) all: 0.44 / Rrim(I) all: 1.183

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158-000refinement
Aimless0.5.25data scaling
XDSOct 15, 2015data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→40.08 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.02 / Stereochemistry target values: ML
Details: Iterative rounds of AK-D158A structure refinement against data extending to 0.176 nm using phenix.refine (Afonine, 2010; Afonine, 2012) of the Phenix program package (version 1.19.2-4158-000) ...Details: Iterative rounds of AK-D158A structure refinement against data extending to 0.176 nm using phenix.refine (Afonine, 2010; Afonine, 2012) of the Phenix program package (version 1.19.2-4158-000) and manual model building with Coot (version 0.9.8.1-EL (Emsley, 2010)) were carried out until the R-free factor and R-factor converged.
RfactorNum. reflection% reflection
Rfree0.2244 2662 5.1 %
Rwork0.181 --
obs0.1832 52151 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.76→40.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3306 0 132 456 3894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133534
X-RAY DIFFRACTIONf_angle_d1.3074797
X-RAY DIFFRACTIONf_dihedral_angle_d15.207580
X-RAY DIFFRACTIONf_chiral_restr0.064537
X-RAY DIFFRACTIONf_plane_restr0.018614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.790.31741440.26662592X-RAY DIFFRACTION100
1.79-1.830.31181510.25122580X-RAY DIFFRACTION100
1.83-1.860.33481390.23662612X-RAY DIFFRACTION100
1.86-1.90.26861410.22342575X-RAY DIFFRACTION100
1.9-1.950.25791380.22542587X-RAY DIFFRACTION100
1.95-20.27661440.2192608X-RAY DIFFRACTION100
2-2.050.27381370.20592596X-RAY DIFFRACTION100
2.05-2.110.24861380.19922597X-RAY DIFFRACTION100
2.11-2.180.23261230.1792597X-RAY DIFFRACTION100
2.18-2.260.19991520.1762569X-RAY DIFFRACTION100
2.26-2.350.21011490.16422598X-RAY DIFFRACTION100
2.35-2.450.25891380.17312592X-RAY DIFFRACTION100
2.45-2.580.23251340.18122631X-RAY DIFFRACTION100
2.58-2.750.24871260.18442624X-RAY DIFFRACTION100
2.75-2.960.23151310.18432611X-RAY DIFFRACTION100
2.96-3.260.23091270.17722613X-RAY DIFFRACTION100
3.26-3.730.18151520.16352626X-RAY DIFFRACTION100
3.73-4.690.17911420.15092615X-RAY DIFFRACTION100
4.69-40.080.20881560.17732666X-RAY DIFFRACTION100

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