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- PDB-6b18: Crystal structure of PPK3 Class III in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 6b18
TitleCrystal structure of PPK3 Class III in complex with inhibitor
ComponentsPPK3 Class III
Keywordstransferase/transferase inhibitor / PPK2 / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-C8A / PHOSPHATE ION / Polyphosphate:AMP phosphotransferase
Similarity search - Component
Biological speciesCytophaga hutchinsonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsNocek, B. / Ruszkowski, M. / Berlicki, L. / Joachimiak, A. / 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
DepositionSep 17, 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 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: PPK3 Class III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1224
Polymers35,5781
Non-polymers5443
Water3,135174
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)111.475, 111.475, 175.733
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-662-

HOH

31A-664-

HOH

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Components

#1: Protein PPK3 Class III


Mass: 35577.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cytophaga hutchinsonii (bacteria) / Strain: ATCC 33406 / NCIMB 9469
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q11YW6
#2: Chemical ChemComp-C8A / {[(4-benzylphenyl)amino]methylene}bis(phosphonic acid)


Mass: 357.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H17NO6P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 3.84 Å3/Da / Density % sol: 67.94 %
Crystal growTemperature: 292 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: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 11, 2013
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. obs: 24690 / % possible obs: 99.6 % / Redundancy: 14.3 % / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.023 / Net I/σ(I): 32.8
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 13.7 % / Rmerge(I) obs: 1.54 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1215 / Rpim(I) all: 0.43 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementResolution: 2.3→94.13 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.913 / SU B: 11.822 / SU ML: 0.145 / Cross valid method: FREE R-VALUE / ESU R: 0.224 / ESU R Free: 0.202 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24101 1169 5.1 %RANDOM
Rwork0.19073 ---
obs0.1933 21885 92.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å2-0 Å2-0 Å2
2--0.19 Å2-0 Å2
3----0.38 Å2
Refinement stepCycle: 1 / Resolution: 2.3→94.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2446 0 34 174 2654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192543
X-RAY DIFFRACTIONr_bond_other_d0.0020.022454
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.9323433
X-RAY DIFFRACTIONr_angle_other_deg0.9382.9885667
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6575300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.25124.874119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.9115481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9821511
X-RAY DIFFRACTIONr_chiral_restr0.0840.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022798
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02579
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_it1.292.4831200
X-RAY DIFFRACTIONr_mcbond_other1.292.4821199
X-RAY DIFFRACTIONr_mcangle_it2.2273.721500
X-RAY DIFFRACTIONr_mcangle_other2.2263.7211501
X-RAY DIFFRACTIONr_scbond_it1.5712.7751342
X-RAY DIFFRACTIONr_scbond_other1.5692.7751342
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.74.0741934
X-RAY DIFFRACTIONr_long_range_B_refined6.07320.6662994
X-RAY DIFFRACTIONr_long_range_B_other6.07320.6662994
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.304→2.364 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 41 -
Rwork0.253 860 -
obs--49.56 %
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)
12.32421.90810.45111.63280.01252.02820.03370.3339-0.4190.11210.1917-0.3151-0.48490.5913-0.22530.1518-0.08180.03960.2715-0.09370.088636.45155.882.4294
20.83580.8771-0.06110.9378-0.00630.78650.1413-0.02650.05580.1245-0.03310.03050.0260.0387-0.10820.10740.08290.04160.12420.0220.114616.3885-4.58018.1549
30.07680.21750.22471.10341.37773.1318-0.03940.0002-0.0445-0.03240.0525-0.1217-0.11150.3555-0.01310.0680.0419-0.00680.1951-0.00570.116228.44915.871515.8426
40.30790.04490.01310.2998-0.08631.1220.0521-0.0129-0.03520.00570.044-0.1405-0.10480.2325-0.09610.07140.03430.03060.1347-0.02390.092924.8896.7461.1523
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 63
2X-RAY DIFFRACTION2A64 - 185
3X-RAY DIFFRACTION3A186 - 209
4X-RAY DIFFRACTION4A210 - 301

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