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- PDB-6au0: Crystal structure of PPK2 (Class III) in complex with bisphosphon... -

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Basic information

Entry
Database: PDB / ID: 6au0
TitleCrystal structure of PPK2 (Class III) in complex with bisphosphonate inhibitor (2-((3,5-dichlorophenyl)amino)ethane-1,1-diyl)diphosphonic acid
ComponentsPolyphosphate:AMP phosphotransferase
Keywordstransferase/transferase inhibitor / PPK2 / kinase / bisphosphonate inhibitor / 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-BWJ / Polyphosphate:AMP phosphotransferase
Similarity search - Component
Biological speciesCytophaga hutchinsonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsNocek, B. / Ruszkowski, M. / Joachimiak, A. / Berlicki, L. / Yakunin, A.
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 29, 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

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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)36,0984
Polymers35,5781
Non-polymers5203
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.355, 109.355, 179.737
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-625-

HOH

21A-626-

HOH

31A-630-

HOH

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Components

#1: Protein Polyphosphate:AMP phosphotransferase


Mass: 35577.523 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-BWJ / {[(3,5-dichlorophenyl)amino]methylene}bis(phosphonic acid)


Mass: 336.003 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9Cl2NO6P2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 3.78 Å3/Da / Density % sol: 67.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 / Details: 0.1 M Phosphate Citrate pH 4.2 40% PEG 300

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 6, 2014
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→100 Å / Num. obs: 32073 / % possible obs: 99.6 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 28.2
Reflection shellResolution: 2.1→2.141 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.91 / Num. unique obs: 1588 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→93.42 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 8.818 / SU ML: 0.113 / Cross valid method: FREE R-VALUE / ESU R: 0.143 / ESU R Free: 0.139 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22048 1622 5.1 %RANDOM
Rwork0.18247 ---
obs0.18435 30340 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 55.396 Å2
Baniso -1Baniso -2Baniso -3
1-1.45 Å2-0 Å20 Å2
2--1.45 Å2-0 Å2
3----2.9 Å2
Refinement stepCycle: 1 / Resolution: 2.1→93.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2451 0 30 134 2615
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192558
X-RAY DIFFRACTIONr_bond_other_d0.0020.022463
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.9353455
X-RAY DIFFRACTIONr_angle_other_deg0.9312.9955692
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8275305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.08525.042119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37815481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3821510
X-RAY DIFFRACTIONr_chiral_restr0.0890.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022828
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02576
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5633.1431217
X-RAY DIFFRACTIONr_mcbond_other1.5633.1431216
X-RAY DIFFRACTIONr_mcangle_it2.494.7041523
X-RAY DIFFRACTIONr_mcangle_other2.4894.7041524
X-RAY DIFFRACTIONr_scbond_it2.3813.531341
X-RAY DIFFRACTIONr_scbond_other2.3763.531341
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8825.1571933
X-RAY DIFFRACTIONr_long_range_B_refined7.34526.172954
X-RAY DIFFRACTIONr_long_range_B_other7.34526.182955
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.099→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 126 -
Rwork0.275 2217 -
obs--99.79 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.36031.21680.37661.1736-0.00651.8637-0.08610.2581-0.2147-0.01390.2079-0.1614-0.33280.6292-0.12190.0958-0.02710.04630.4794-0.07970.139936.13236.351.5313
20.03690.1707-0.02381.0420.03073.0972-0.012-0.0385-0.0433-0.0271-0.0308-0.0773-0.1799-0.01270.04280.14940.06650.00980.3119-0.00730.201522.40286.47794.2144
33.54832.9695-3.54333.9566-2.92243.55110.2396-0.15680.19750.0547-0.09510.3723-0.19390.164-0.14450.20130.05920.03780.21380.00070.23410.11633.19895.9226
40.91430.6737-0.00631.0519-0.91051.51830.1294-0.10520.17910.0451-0.08850.11560.10150.0841-0.04090.18860.07670.0170.2673-0.0150.226814.9255-4.83599.1684
58.0820.12033.1530.6318-0.94473.0060.5031-0.8366-0.13890.0402-0.29660.07240.2005-0.0805-0.20650.2676-0.0636-0.01020.38660.04480.123811.4013-16.519720.7756
60.66230.49230.36530.63580.48210.55420.04640.0077-0.10470.01630.0387-0.15970.15710.2487-0.08510.16680.1386-0.02130.28790.00890.25622.51-9.49385.3986
75.2308-2.9345-0.82156.29141.57910.4194-0.1384-0.18710.00050.37780.1180.04360.03640.08720.02040.2843-0.0089-0.06440.3183-0.0320.049825.250114.673523.8334
80.39790.0176-0.89893.75073.10774.91380.1765-0.0527-0.12660.2394-0.1736-0.1742-0.0351-0.0149-0.0030.19030.0728-0.14530.36920.0450.15926.1795-3.125721.0995
90.66480.23590.86390.4643-0.04141.5569-0.02250.1882-0.05430.02040.0092-0.1215-0.04080.51370.01330.07010.04950.01110.4268-0.0460.220531.84253.90541.7954
100.8098-1.1755-0.27972.5672-1.27833.47210.04620.0757-0.21120.26150.03860.3181-0.8624-0.51-0.08480.25250.13230.05180.51710.040.164416.692317.3361-30.389
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 64
2X-RAY DIFFRACTION2A65 - 91
3X-RAY DIFFRACTION3A92 - 111
4X-RAY DIFFRACTION4A112 - 150
5X-RAY DIFFRACTION5A151 - 164
6X-RAY DIFFRACTION6A165 - 197
7X-RAY DIFFRACTION7A198 - 219
8X-RAY DIFFRACTION8A220 - 243
9X-RAY DIFFRACTION9A244 - 276
10X-RAY DIFFRACTION10A277 - 301

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