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- PDB-9r71: Crystal structure of E. coli Adenylate kinase E114A mutant in com... -

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Basic information

Entry
Database: PDB / ID: 9r71
TitleCrystal structure of E. coli Adenylate kinase E114A mutant in complex with inhibitor Ap5a.
ComponentsAdenylate kinase
KeywordsTRANSFERASE / ADENYLATE KINASE / E114A 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: 1.61 Å
AuthorsMattsson, J. / Rogne, P. / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,9574
Polymers47,1242
Non-polymers1,8332
Water6,557364
1
A: 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
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)72.962, 84.516, 78.931
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: 23561.994 Da / Num. of mol.: 2
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: obtained synthetically / Formula: C20H29N10O22P5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.58 Å3/Da / Density % sol: 52.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium acetate, 0.1 M sodium citrate tribasic dihydrate pH 4.6, and 32% (w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.8731 Å
DetectorType: PSI JUNGFRAU 4M / Detector: PIXEL / Date: Jul 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.61→57.69 Å / Num. obs: 63456 / % possible obs: 99.7 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.029 / Net I/σ(I): 14.2
Reflection shellResolution: 1.61→1.64 Å / Rmerge(I) obs: 2.496 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3017 / CC1/2: 0.51 / Rpim(I) all: 0.707 / % possible all: 96.8

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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: 1.61→57.69 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.244 3202 5.05 %
Rwork0.193 --
obs0.196 63405 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.61→57.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3304 0 114 364 3782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033499
X-RAY DIFFRACTIONf_angle_d0.754751
X-RAY DIFFRACTIONf_dihedral_angle_d14.511538
X-RAY DIFFRACTIONf_chiral_restr0.042529
X-RAY DIFFRACTIONf_plane_restr0.004606
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.640.40621380.33512492X-RAY DIFFRACTION96
1.64-1.660.3681520.32532582X-RAY DIFFRACTION100
1.66-1.690.39281440.30542594X-RAY DIFFRACTION100
1.69-1.720.36391400.29172564X-RAY DIFFRACTION100
1.72-1.750.38421630.26732560X-RAY DIFFRACTION100
1.75-1.780.30121260.24162613X-RAY DIFFRACTION100
1.78-1.820.3241300.24282616X-RAY DIFFRACTION100
1.82-1.860.32341470.23362561X-RAY DIFFRACTION100
1.86-1.90.2591310.22432597X-RAY DIFFRACTION100
1.9-1.950.26721140.21972629X-RAY DIFFRACTION100
1.95-20.3191290.21572612X-RAY DIFFRACTION100
2-2.060.28011380.21412627X-RAY DIFFRACTION100
2.06-2.130.28351320.21752584X-RAY DIFFRACTION100
2.13-2.20.29061210.19682626X-RAY DIFFRACTION100
2.2-2.290.26191350.19542621X-RAY DIFFRACTION100
2.29-2.40.26161290.18442634X-RAY DIFFRACTION100
2.4-2.520.22031410.19122617X-RAY DIFFRACTION100
2.52-2.680.2561530.19112606X-RAY DIFFRACTION100
2.68-2.890.28361310.20142655X-RAY DIFFRACTION100
2.89-3.180.27661290.18622665X-RAY DIFFRACTION100
3.18-3.640.21561500.17872654X-RAY DIFFRACTION100
3.64-4.590.1881810.15512662X-RAY DIFFRACTION100
4.59-57.690.19231480.17452832X-RAY DIFFRACTION100

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