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- PDB-6aqn: Crystal structure of PPK2 in complex with phosphonic acid inhibitor -

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Basic information

Entry
Database: PDB / ID: 6aqn
TitleCrystal structure of PPK2 in complex with phosphonic acid inhibitor
ComponentsPolyphosphate:AMP phosphotransferase
Keywordstransferase/transferase inhibitor / PPK2 / Kinase / Inhibitor / (hydroxy(p-toluyl)methyl)phosphonic acid / TRANSFERASE / transferase-transferase inhibitor complex
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor / polyphosphate kinase activity / polyphosphate metabolic process
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
Chem-BOY / S,R MESO-TARTARIC ACID / Polyphosphate:AMP phosphotransferase
Similarity search - Component
Biological speciesCytophaga hutchinsonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.199 Å
AuthorsNocek, B. / Berlicki, l. / Joachimiak, A. / Yakunin, S.
CitationJournal: Acs Catalysis / Year: 2018
Title: Structural Insights into Substrate Selectivity and Activity of Bacterial Polyphosphate Kinases
Authors: Nocek, B. / Khusnutdinova, A.N. / Ruszkowski, M. / Flick, R. / Burda, M. / Batyrova, K. / Brown, G. / Mucha, A. / Joachimiak, A. / Berlicki, L. / Yakunin, A.F.
History
DepositionAug 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 4, 2023Group: 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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyphosphate:AMP phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9844
Polymers35,5401
Non-polymers4443
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-1 kcal/mol
Surface area15570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.761, 110.761, 177.814
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-656-

HOH

21A-664-

HOH

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Components

#1: Protein Polyphosphate:AMP phosphotransferase / molecule 1


Mass: 35539.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cytophaga hutchinsonii (strain ATCC 33406 / NCIMB 9469) (bacteria)
Strain: ATCC 33406 / NCIMB 9469 / Gene: CHU_0107
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q11YW6, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor
#2: Chemical ChemComp-BOY / [(R)-hydroxy(4-methylphenyl)methyl]phosphonic acid


Mass: 202.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11O4P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 3.9 Å3/Da / Density % sol: 68.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 60% Tacsimate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 10, 2015 / Details: double mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.199→35.03 Å / Num. obs: 28376 / % possible obs: 99.6 % / Redundancy: 5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 28
Reflection shellResolution: 2.199→2.29 Å

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Processing

Software
NameVersionClassification
PHENIX(dev_2363: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ANG

6ang


Resolution: 2.199→35.026 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.63 / Phase error: 28.91
RfactorNum. reflection% reflectionSelection details
Rfree0.2507 1250 5.09 %0.21
Rwork0.2032 ---
obs0.2056 24559 92.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.199→35.026 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2408 0 29 181 2618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032486
X-RAY DIFFRACTIONf_angle_d0.5923367
X-RAY DIFFRACTIONf_dihedral_angle_d15.9041480
X-RAY DIFFRACTIONf_chiral_restr0.041380
X-RAY DIFFRACTIONf_plane_restr0.003425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1993-2.28730.2688560.2588878X-RAY DIFFRACTION30
2.2873-2.39140.3405800.27131690X-RAY DIFFRACTION57
2.3914-2.51750.27731320.26522792X-RAY DIFFRACTION93
2.5175-2.67510.33961470.26652939X-RAY DIFFRACTION99
2.6751-2.88160.28731710.26082951X-RAY DIFFRACTION99
2.8816-3.17140.27961750.23982959X-RAY DIFFRACTION99
3.1714-3.62990.2521620.20272962X-RAY DIFFRACTION99
3.6299-4.57170.2091550.15683016X-RAY DIFFRACTION99
4.5717-35.03010.21881720.17063122X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1899-0.10350.07660.3736-0.29040.4851-0.0669-0.0833-0.0040.28630.44210.3409-0.4088-0.54270.27690.0254-0.09280.05860.53410.12180.376119.59226.835942.6261
20.2816-0.2390.26720.4785-0.39970.39710.05780.0770.0209-0.11030.02280.04920.0462-0.092900.1932-0.0910.01380.2599-0.01440.219638.0242-4.125736.9277
30.00430.0073-0.01230.01990.01170.01870.01560.0552-0.01670.12140.0486-0.0951-0.2426-0.08200.4343-0.0348-0.08190.46610.10330.377231.265714.891120.6441
40.39020.0593-0.23430.5632-0.39620.4170.06460.00540.0257-0.05190.05090.1699-0.0679-0.34920.00050.1537-0.03330.02480.3120.01260.256630.16065.726846.6773
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 63 )
2X-RAY DIFFRACTION2chain 'A' and (resid 64 through 197 )
3X-RAY DIFFRACTION3chain 'A' and (resid 198 through 219 )
4X-RAY DIFFRACTION4chain 'A' and (resid 220 through 302 )

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