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- PDB-8pvw: Structure of a short E. coli adenylate kinase in complex with Ap5A -

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Basic information

Entry
Database: PDB / ID: 8pvw
TitleStructure of a short E. coli adenylate kinase in complex with Ap5A
ComponentsAdenylate kinase
KeywordsSIGNALING PROTEIN / P-loop nucleotide/nucleoside kinase-like
Function / homologyBIS(ADENOSINE)-5'-PENTAPHOSPHATE
Function and homology information
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRodriguez, J.A. / Wolf Watz, M. / Sauer-Eriksson, E.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2021-04513_VR Sweden
CitationJournal: To Be Published
Title: Structure of a short E. coli adenylate kinase in complex with Ap5A
Authors: Rodriguez, J.A. / Wolf Watz, M. / Nagy, T.M. / Phoeurk, C. / Rogne, P. / Schierholz, L.J.
History
DepositionJul 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4572
Polymers20,5411
Non-polymers9161
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-6 kcal/mol
Surface area9430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.838, 73.244, 90.357
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Adenylate kinase


Mass: 20540.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: BL21 / Gene: adk, dnaW, plsA, b0474, JW0463 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: adenylate kinase
#2: Chemical ChemComp-AP5 / BIS(ADENOSINE)-5'-PENTAPHOSPHATE


Mass: 916.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H29N10O22P5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.49 Å3/Da / Density % sol: 50 % / Description: Plate
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 30% PEG 4000, 0.2 M Ammonium sulfate / PH range: 7.0-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.873 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.7→58.45 Å / Num. obs: 13571 / % possible obs: 78.7 % / Redundancy: 10 % / Biso Wilson estimate: 18.36 Å2 / CC1/2: 0.988 / CC star: 0.988 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.036 / Net I/σ(I): 12.4
Reflection shellResolution: 1.955→2.5 Å / Num. unique obs: 13571 / CC1/2: 0.988

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→38.45 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2344 620 5 %
Rwork0.1834 --
obs0.1859 12390 85.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→38.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1438 0 57 114 1609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141525
X-RAY DIFFRACTIONf_angle_d1.7252069
X-RAY DIFFRACTIONf_dihedral_angle_d21.184238
X-RAY DIFFRACTIONf_chiral_restr0.062232
X-RAY DIFFRACTIONf_plane_restr0.008262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.20.29521040.24132031X-RAY DIFFRACTION60
2.2-2.520.27871430.19863087X-RAY DIFFRACTION91
2.52-3.170.26021960.20033288X-RAY DIFFRACTION97
3.17-38.450.20341770.16413365X-RAY DIFFRACTION94

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