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- PDB-6aqe: Crystal structure of PPK2 in complex with Mg ATP -

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Basic information

Entry
Database: PDB / ID: 6aqe
TitleCrystal structure of PPK2 in complex with Mg ATP
Componentsmolecule A
KeywordsTRANSFERASE / PPK2 / Kinase / Mg / ATP
Function / homology
Function and homology information


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
ADENOSINE-5'-TRIPHOSPHATE / PPK2 domain-containing protein
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.805 Å
AuthorsNocek, B. / Joachimiak, A. / Yakunin, A.
CitationJournal: Acs Catalysis / Year: 2018
Title: Structural Insights into Substrate Selectivity and Activity of Bacterial Polyphosphate Kinases
Authors: Nocek, B.P. / Khusnutdinova, A.N. / Ruszkowski, M. / Flick, R. / Burda, M. / Batyrova, K. / Brown, G. / Mucha, A. / Joachimiak, A. / Berlicki, L. / Yakunin, A.F.
History
DepositionAug 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: 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

Downloads & links

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Assembly

Deposited unit
A: molecule A
B: molecule A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,95718
Polymers61,0992
Non-polymers2,85816
Water9,584532
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homotetramer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9340 Å2
ΔGint-92 kcal/mol
Surface area23100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.376, 88.376, 190.016
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-830-

HOH

21B-799-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein molecule A


Mass: 30549.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: DR_0132
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9RY20

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Non-polymers , 6 types, 548 molecules

#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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 532 / 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: 3.04 Å3/Da / Density % sol: 59.49 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2 M CaCl2 0.1 M BisTris 45% MPD

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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 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.81→39.5 Å / Num. obs: 69957 / % possible obs: 100 % / Redundancy: 12.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 22
Reflection shellResolution: 1.81→1.84 Å / % possible all: 100

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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: 3RHF
Resolution: 1.805→39.523 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1864 3510 5.04 %
Rwork0.1615 --
obs0.1628 69615 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.805→39.523 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4307 0 175 532 5014
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0184638
X-RAY DIFFRACTIONf_angle_d1.6186313
X-RAY DIFFRACTIONf_dihedral_angle_d18.1162783
X-RAY DIFFRACTIONf_chiral_restr0.103659
X-RAY DIFFRACTIONf_plane_restr0.009798
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8045-1.82920.24971280.22212495X-RAY DIFFRACTION97
1.8292-1.85540.231400.21382593X-RAY DIFFRACTION100
1.8554-1.88310.28911230.20882640X-RAY DIFFRACTION100
1.8831-1.91250.24411490.19612606X-RAY DIFFRACTION100
1.9125-1.94380.25041570.20032589X-RAY DIFFRACTION100
1.9438-1.97740.22951500.18692622X-RAY DIFFRACTION100
1.9774-2.01330.20361570.1782621X-RAY DIFFRACTION100
2.0133-2.0520.21511420.1752596X-RAY DIFFRACTION100
2.052-2.09390.22821330.17742609X-RAY DIFFRACTION100
2.0939-2.13950.20571660.1752590X-RAY DIFFRACTION100
2.1395-2.18920.18291180.16662621X-RAY DIFFRACTION100
2.1892-2.2440.21821460.16652621X-RAY DIFFRACTION99
2.244-2.30460.22151270.17022633X-RAY DIFFRACTION99
2.3046-2.37240.17761370.1632585X-RAY DIFFRACTION99
2.3724-2.4490.20141540.16362658X-RAY DIFFRACTION99
2.449-2.53650.20341340.17362609X-RAY DIFFRACTION99
2.5365-2.63810.2081250.17152650X-RAY DIFFRACTION99
2.6381-2.75810.2081470.16252643X-RAY DIFFRACTION99
2.7581-2.90350.17781280.15532659X-RAY DIFFRACTION100
2.9035-3.08530.15921310.14562670X-RAY DIFFRACTION100
3.0853-3.32340.17081290.1442679X-RAY DIFFRACTION100
3.3234-3.65760.16041440.13762708X-RAY DIFFRACTION100
3.6576-4.18640.15031630.13082704X-RAY DIFFRACTION100
4.1864-5.27240.13631350.14492774X-RAY DIFFRACTION100
5.2724-39.53240.22371470.19592930X-RAY DIFFRACTION100
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)
11.1142-0.824-1.57841.22161.35392.21160.01410.1334-0.0055-0.1418-0.04230.29070.0563-0.44390.02740.2382-0.006-0.02390.2903-0.00860.280651.19166.83644.724
26.9651-2.5835-5.69064.27855.1118.1494-0.3095-0.2898-0.43640.36830.03710.41870.29950.07730.26010.24620.0129-0.02690.20350.0870.191562.028351.889318.1844
31.779-1.5188-0.57717.93971.13491.9942-0.0286-0.14690.0322-0.00280.10330.0731-0.01750.1074-0.10330.1060.0015-0.00260.21710.02370.1867.812162.98769.0185
40.71760.297-0.58331.0481-0.84241.4381-0.0086-0.0780.01030.0834-0.0133-0.0526-0.13120.11140.00070.1894-0.0007-0.02060.1896-0.01050.179374.961865.37810.7253
51.8267-1.13980.31973.0609-1.6311.30860.07270.1860.0246-0.3572-0.02810.23870.0375-0.1122-0.03990.20240.0067-0.01510.2201-0.02390.159567.838762.6904-10.6727
60.632-0.07240.17361.47280.93451.6611-0.0366-0.03730.1321-0.06930.028-0.0265-0.21130.00870.04260.19740.01110.02520.20770.0090.208165.230577.17648.0557
70.8981-0.6785-0.44872.11620.78732.09420.0011-0.075-0.06090.07580.09580.02850.0877-0.1430.00480.1462-0.0022-0.00320.20590.010.208958.410160.44229.3548
83.3227-3.61273.65333.8618-3.80353.74671.08550.0524-0.9024-0.9772-0.28620.34391.390.2945-0.65480.51640.033-0.16070.33190.07850.566673.422130.158116.2641
90.8283-0.39170.13672.1134-0.76990.8474-0.0518-0.25050.02560.26730.08170.1043-0.1044-0.1689-0.02740.27770.0048-0.00490.304-0.02020.213186.281957.455734.1968
100.847-0.1581-0.31410.88950.23341.11420.02360.052-0.0058-0.0538-0.02020.0818-0.0209-0.19060.0150.1812-0.0033-0.03270.20540.00420.196287.674354.942115.3299
111.57310.7657-0.36085.4621-0.49071.26910.01510.0068-0.1658-0.0225-0.0918-0.30250.17040.03340.06090.1935-0.0071-0.02270.21920.0040.1588101.521748.660216.7399
121.158-0.30420.36810.2297-0.2660.6635-0.011-0.097-0.0543-0.01450.02490.03160.0113-0.0876-0.03550.1982-0.00530.00650.22890.01360.174185.695652.022925.8838
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 28 )
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 53 )
3X-RAY DIFFRACTION3chain 'A' and (resid 54 through 76 )
4X-RAY DIFFRACTION4chain 'A' and (resid 77 through 138 )
5X-RAY DIFFRACTION5chain 'A' and (resid 139 through 159 )
6X-RAY DIFFRACTION6chain 'A' and (resid 160 through 216 )
7X-RAY DIFFRACTION7chain 'A' and (resid 217 through 249 )
8X-RAY DIFFRACTION8chain 'A' and (resid 250 through 266 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 53 )
10X-RAY DIFFRACTION10chain 'B' and (resid 54 through 121 )
11X-RAY DIFFRACTION11chain 'B' and (resid 122 through 159 )
12X-RAY DIFFRACTION12chain 'B' and (resid 160 through 266 )

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