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- PDB-6an9: Crystal structure of PPk2 class III in complex with ADP from Cyto... -

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Basic information

Entry
Database: PDB / ID: 6an9
TitleCrystal structure of PPk2 class III in complex with ADP from Cytophaga hutchinsonii ATCC 33406
ComponentsPolyphosphate:AMP phosphotransferase
KeywordsTRANSFERASE / PPK2 / polyphosphate kinase / ADP-binding
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
ADENOSINE-5'-DIPHOSPHATE / Polyphosphate:AMP phosphotransferase
Similarity search - Component
Biological speciesCytophaga hutchinsonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.891 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. / Khusnutdinova, A.N. / Ruszkowski, M. / Flick, R. / Burda, M. / Batyrova, K. / Brown, G. / Mucha, A. / Joachimiak, A. / Berlicki, L. / Yakunin, A.F.
History
DepositionAug 12, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyphosphate:AMP phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8253
Polymers35,3051
Non-polymers5192
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-3 kcal/mol
Surface area15470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.121, 111.121, 178.562
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-2243-

HOH

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Components

#1: Protein Polyphosphate:AMP phosphotransferase


Mass: 35305.270 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-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 68.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.1 M Ammonium tartrate dibasic

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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 / Details: double mirror
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.89→39.3 Å / Num. obs: 44492 / % possible obs: 99.3 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 23
Reflection shellResolution: 1.89→1.93 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

3rhf


Resolution: 1.891→39.287 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0.64 / Phase error: 19.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2054 2242 5.06 %
Rwork0.1762 --
obs0.1777 44346 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.891→39.287 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2373 0 33 152 2558
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192489
X-RAY DIFFRACTIONf_angle_d1.4523383
X-RAY DIFFRACTIONf_dihedral_angle_d16.2521485
X-RAY DIFFRACTIONf_chiral_restr0.082380
X-RAY DIFFRACTIONf_plane_restr0.01428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8911-1.93220.26811430.2592510X-RAY DIFFRACTION97
1.9322-1.97710.2541490.22552615X-RAY DIFFRACTION100
1.9771-2.02660.23031470.20382603X-RAY DIFFRACTION100
2.0266-2.08130.22881520.19932609X-RAY DIFFRACTION100
2.0813-2.14260.24481480.19182610X-RAY DIFFRACTION99
2.1426-2.21170.21361420.18642632X-RAY DIFFRACTION100
2.2117-2.29080.21291310.17772626X-RAY DIFFRACTION100
2.2908-2.38250.22951350.18322639X-RAY DIFFRACTION99
2.3825-2.49090.22981360.17862637X-RAY DIFFRACTION100
2.4909-2.62220.24481430.18842623X-RAY DIFFRACTION99
2.6222-2.78640.29181380.20592647X-RAY DIFFRACTION99
2.7864-3.00150.23591260.20052683X-RAY DIFFRACTION99
3.0015-3.30340.2241350.19672660X-RAY DIFFRACTION99
3.3034-3.78110.18641620.16712647X-RAY DIFFRACTION99
3.7811-4.76250.13341360.13012680X-RAY DIFFRACTION98
4.7625-39.29570.19821190.17232683X-RAY DIFFRACTION93
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)
10.1879-0.0280.13250.1386-0.16450.3066-0.04530.0299-0.1321-0.00590.28550.46210.1065-0.81350.29070.2553-0.057800.77030.0980.481815.90051.4737.7148
20.0256-0.076-0.01950.08450.1440.0769-0.0804-0.14040.2620.05410.0108-0.1796-0.2582-0.14710.00010.31910.00420.05430.4728-0.01030.335526.541914.821149.9907
30.1239-0.17340.01890.2840.1170.0266-0.0526-0.1040.07570.0113-0.0424-0.038-0.2039-0.437300.31450.0113-0.00670.38770.01840.333133.43996.896640.4819
40.6708-0.32960.00430.7086-0.35720.68990.08030.0553-0.0183-0.0924-0.00520.0070.138-0.1354-00.2522-0.0972-0.00920.30980.00010.284339.51-6.414436.1565
50.03160.0131-0.04270.0052-0.03080.06270.0983-0.03460.2382-0.0173-0.0516-0.0654-0.3912-0.4282-00.45570.0049-0.04190.53590.05930.409731.343815.068920.6415
60.1567-0.18770.05610.31080.18470.2270.0270.0513-0.0899-0.11060.11730.04740.0687-0.50370.00070.2894-0.1093-0.04610.46510.02480.340527.6701-2.775929.1471
70.0372-0.03310.03530.06710.05850.04320.03910.0875-0.12540.1269-0.07990.1216-0.2723-0.3262-0.00010.25010.0297-0.00240.50990.04550.342423.43817.748544.938
80.06140.1051-0.16940.0165-0.08140.188-0.02260.0947-0.3609-0.0840.302-0.2577-0.4748-0.0441-0.00010.4372-0.05470.05290.5289-0.05470.366239.200717.226375.2547
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 39 )
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 63 )
3X-RAY DIFFRACTION3chain 'A' and (resid 64 through 91 )
4X-RAY DIFFRACTION4chain 'A' and (resid 92 through 197 )
5X-RAY DIFFRACTION5chain 'A' and (resid 198 through 219 )
6X-RAY DIFFRACTION6chain 'A' and (resid 220 through 257 )
7X-RAY DIFFRACTION7chain 'A' and (resid 258 through 276 )
8X-RAY DIFFRACTION8chain 'A' and (resid 277 through 302 )

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