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- PDB-6ang: Crystal structure of PPK2 Class III in the complex with AMP from ... -

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Basic information

Entry
Database: PDB / ID: 6ang
TitleCrystal structure of PPK2 Class III in the complex with AMP from Cytophaga hutchinsonii ATCC 33406
ComponentsPolyphosphate:AMP phosphotransferase
KeywordsTRANSFERASE / PPK2 / AMP / kinase
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
ADENOSINE MONOPHOSPHATE / Polyphosphate:AMP phosphotransferase
Similarity search - Component
Biological speciesCytophaga hutchinsonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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 13, 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

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Assembly

Deposited unit
A: Polyphosphate:AMP phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6883
Polymers35,3051
Non-polymers3832
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homotetramer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.224, 111.224, 177.694
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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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-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 101 / 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: 3.89 Å3/Da / Density % sol: 68.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.8 Ammonium Sulfate 0.1M NaCL 0.1 M Sodium Citrate:HCl pH 4

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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: Jan 1, 2016
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.45→40 Å / Num. obs: 20573 / % possible obs: 98.5 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 12
Reflection shellResolution: 2.45→2.49 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RHF

3rhf


Resolution: 2.45→39.32 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.927 / SU B: 6.95 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.213 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22018 966 5.1 %RANDOM
Rwork0.18955 ---
obs0.19115 17937 90.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.458 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2--0.12 Å20 Å2
3----0.24 Å2
Refinement stepCycle: 1 / Resolution: 2.45→39.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2410 0 24 102 2536
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192480
X-RAY DIFFRACTIONr_bond_other_d0.0020.022375
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.9643355
X-RAY DIFFRACTIONr_angle_other_deg1.07635480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2985296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.81525.043115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.26115459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.131510
X-RAY DIFFRACTIONr_chiral_restr0.1040.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022743
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02558
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_it3.4573.5261187
X-RAY DIFFRACTIONr_mcbond_other3.4373.5251186
X-RAY DIFFRACTIONr_mcangle_it5.1815.2791482
X-RAY DIFFRACTIONr_mcangle_other5.1855.2811483
X-RAY DIFFRACTIONr_scbond_it5.1234.0781293
X-RAY DIFFRACTIONr_scbond_other5.1214.0771294
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.1455.8471874
X-RAY DIFFRACTIONr_long_range_B_refined10.6633.34310503
X-RAY DIFFRACTIONr_long_range_B_other10.65633.34410459
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.451→2.515 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 52 -
Rwork0.264 616 -
obs--44.09 %

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