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- PDB-5o6m: Structure of Polyphosphate Kinase from Meiothermus ruber N121D bo... -

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Basic information

Entry
Database: PDB / ID: 5o6m
TitleStructure of Polyphosphate Kinase from Meiothermus ruber N121D bound to ATP
ComponentsPolyphosphate:AMP phosphotransferase
KeywordsTRANSFERASE / Polyphosphate Kinase type 2 class III
Function / homology
Function and homology information


phosphotransferase activity, phosphate group as acceptor / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor / polyphosphate kinase activity / polyphosphate metabolic process / kinase activity / phosphorylation
Similarity search - Function
Polyphosphate:nucleotide phosphotransferase, PPK2 / Polyphosphate phosphotransferase / Polyphosphate kinase-2-related / Polyphosphate kinase 2 (PPK2) / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / Polyphosphate:AMP phosphotransferase / AMP/ADP-polyphosphate phosphotransferase
Similarity search - Component
Biological speciesMeiothermus ruber H328 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKemper, F. / Gerhardt, S. / Einsle, O.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Substrate recognition and mechanism revealed by ligand-bound polyphosphate kinase 2 structures.
Authors: Parnell, A.E. / Mordhorst, S. / Kemper, F. / Giurrandino, M. / Prince, J.P. / Schwarzer, N.J. / Hofer, A. / Wohlwend, D. / Jessen, H.J. / Gerhardt, S. / Einsle, O. / Oyston, P.C.F. / Andexer, J.N. / Roach, P.L.
History
DepositionJun 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyphosphate:AMP phosphotransferase
B: Polyphosphate:AMP phosphotransferase
C: Polyphosphate:AMP phosphotransferase
D: Polyphosphate:AMP phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,55030
Polymers126,4324
Non-polymers4,11826
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18900 Å2
ΔGint-184 kcal/mol
Surface area43520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.620, 164.620, 95.125
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Polyphosphate:AMP phosphotransferase


Mass: 31607.961 Da / Num. of mol.: 4 / Mutation: N121D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meiothermus ruber H328 (bacteria) / Gene: MrH_2468 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S7ASE9, UniProt: M9XB82*PLUS
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical...
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O

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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: 2.55 Å3/Da / Density % sol: 51.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Tris/HCl pH 8.5 200 mM Li2SO4 27 % (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 9, 2017 / Details: MIRROR
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→47.56 Å / Num. obs: 58486 / % possible obs: 100 % / Redundancy: 26.4 % / CC1/2: 1 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.026 / Net I/σ(I): 22.1
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 27.6 % / Rmerge(I) obs: 1.659 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 4452 / CC1/2: 0.928 / Rpim(I) all: 0.32 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LC9

5lc9


Resolution: 2.3→47.532 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2386 2818 4.83 %RANDOM
Rwork0.1949 ---
obs0.1971 58336 99.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→47.532 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8732 0 234 294 9260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039276
X-RAY DIFFRACTIONf_angle_d0.612587
X-RAY DIFFRACTIONf_dihedral_angle_d18.4625577
X-RAY DIFFRACTIONf_chiral_restr0.0421297
X-RAY DIFFRACTIONf_plane_restr0.0031667
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.33970.31181220.25032733X-RAY DIFFRACTION100
2.3397-2.38220.26951410.22922746X-RAY DIFFRACTION100
2.3822-2.4280.26881520.22152701X-RAY DIFFRACTION100
2.428-2.47760.25541230.22092746X-RAY DIFFRACTION100
2.4776-2.53150.26531280.2262756X-RAY DIFFRACTION100
2.5315-2.59040.29711580.22142730X-RAY DIFFRACTION100
2.5904-2.65510.24191330.21452748X-RAY DIFFRACTION100
2.6551-2.72690.29451330.21982754X-RAY DIFFRACTION100
2.7269-2.80710.30991400.23062740X-RAY DIFFRACTION100
2.8071-2.89770.29881620.23462724X-RAY DIFFRACTION100
2.8977-3.00130.29131420.22792744X-RAY DIFFRACTION100
3.0013-3.12140.2761430.21842762X-RAY DIFFRACTION100
3.1214-3.26350.27321600.21312771X-RAY DIFFRACTION100
3.2635-3.43550.20841280.21012767X-RAY DIFFRACTION100
3.4355-3.65060.23721250.1912808X-RAY DIFFRACTION100
3.6506-3.93240.21291310.17932800X-RAY DIFFRACTION100
3.9324-4.32790.21031450.16032816X-RAY DIFFRACTION100
4.3279-4.95360.20131710.15962791X-RAY DIFFRACTION100
4.9536-6.23870.23081340.18172868X-RAY DIFFRACTION100
6.2387-47.5420.21241470.18533013X-RAY DIFFRACTION100

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