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- PDB-9r6u: Crystal structure of E. coli Adenylate kinase K47A mutant in comp... -

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Basic information

Entry
Database: PDB / ID: 9r6u
TitleCrystal structure of E. coli Adenylate kinase K47A mutant in complex with inhibitor Ap5A
ComponentsAdenylate kinase
KeywordsTRANSFERASE / ADENYLATE KINASE / K47A mutant / AP5A / PROTEIN DYNAMICS
Function / homology
Function and homology information


adenylate kinase / AMP kinase activity / AMP salvage / ATP binding / cytoplasm
Similarity search - Function
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 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: 1.77 Å
AuthorsPhoeurk, C. / Wolf-Watz, M. / Sauer-Eriksson, A.E.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Biochemistry / Year: 2025
Title: Exploring Helical Fraying Linked to Dynamics and Catalysis in Adenylate Kinase.
Authors: Mattsson, J. / Phoeurk, C. / Schierholz, L. / Mushtaq, A.U. / Rodriguez Buitrago, J.A. / Rogne, P. / Sauer-Eriksson, A.E. / Wolf-Watz, M.
History
DepositionMay 13, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 29, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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)49,0726
Polymers47,1242
Non-polymers1,9484
Water7,224401
1
A: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5934
Polymers23,5621
Non-polymers1,0313
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4782
Polymers23,5621
Non-polymers9161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.763, 79.057, 83.115
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

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


Mass: 23561.928 Da / Num. of mol.: 2 / Mutation: K47A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: adk, EcE24377A_0513 / Production host: Escherichia coli (E. coli) / References: UniProt: A7ZIN4, adenylate kinase
#2: Chemical ChemComp-AP5 / BIS(ADENOSINE)-5'-PENTAPHOSPHATE


Mass: 916.367 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C20H29N10O22P5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.57 Å3/Da / Density % sol: 52.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 30% (w/v) PEG 4000, 0.2 M ammonium sulfate, 0.1 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.77→45.24 Å / Num. obs: 45314 / % possible obs: 94.4 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.048 / Net I/σ(I): 12.4
Reflection shellResolution: 1.77→1.83 Å / Redundancy: 3.2 % / Num. unique obs: 3309 / CC1/2: 0.324 / % possible all: 70

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
Aimlessdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→45.24 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / Phase error: 24.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2279 2366 5.23 %
Rwork0.1919 --
obs-45207 94.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.77→45.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3304 0 121 401 3826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083618
X-RAY DIFFRACTIONf_angle_d1.1234932
X-RAY DIFFRACTIONf_dihedral_angle_d16.928508
X-RAY DIFFRACTIONf_chiral_restr0.051542
X-RAY DIFFRACTIONf_plane_restr0.007623
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.830.47150.45133309X-RAY DIFFRACTION70
1.81-1.850.42761140.37741974X-RAY DIFFRACTION74
1.85-1.890.34251200.28332325X-RAY DIFFRACTION88
1.89-1.940.30181430.23552525X-RAY DIFFRACTION96
1.94-1.990.27151340.20652639X-RAY DIFFRACTION99
1.99-2.050.25361380.1942643X-RAY DIFFRACTION99
2.05-2.110.24021250.19392654X-RAY DIFFRACTION99
2.11-2.190.2231120.18432666X-RAY DIFFRACTION99
2.19-2.280.23431470.17372647X-RAY DIFFRACTION100
2.28-2.380.20531490.17012638X-RAY DIFFRACTION99
2.38-2.50.2331480.17662633X-RAY DIFFRACTION99
2.5-2.660.23291610.18512653X-RAY DIFFRACTION99
2.66-2.870.26321410.18952642X-RAY DIFFRACTION98
2.87-3.150.22481600.18712599X-RAY DIFFRACTION97
3.16-3.610.21661130.1662408X-RAY DIFFRACTION88
3.61-4.550.17261590.13982671X-RAY DIFFRACTION98
4.55-45.240.18031770.16682785X-RAY DIFFRACTION98

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