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- PDB-6anh: Crystal structure of PPK2 class III in complex with Guanosine 5-t... -

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Basic information

Entry
Database: PDB / ID: 6anh
TitleCrystal structure of PPK2 class III in complex with Guanosine 5-tetraphosphate
ComponentsPolyphosphate:AMP phosphotransferase
KeywordsTRANSFERASE / PPK2 / kinase / Guanosine 5-tetraphosphate
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-BKP / Polyphosphate:AMP phosphotransferase
Similarity search - Component
Biological speciesCytophaga hutchinsonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 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 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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)36,1432
Polymers35,5401
Non-polymers6031
Water54030
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)110.812, 110.812, 178.807
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-526-

HOH

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Components

#1: Protein Polyphosphate:AMP phosphotransferase


Mass: 35539.742 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 (E. coli)
References: UniProt: Q11YW6, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor
#2: Chemical ChemComp-BKP / 5'-O-[(S)-hydroxy{[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]oxy}phosphoryl]guanosine


Mass: 603.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N5O17P4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.92 Å3/Da / Density % sol: 68.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging 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: Aug 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.6→36.2 Å / Num. obs: 17542 / % possible obs: 99.8 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 25
Reflection shellResolution: 2.65→2.74 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.65→36.17 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 10.719 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.339 / ESU R Free: 0.255 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23813 825 5 %RANDOM
Rwork0.19398 ---
obs0.19616 15516 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 65 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.65→36.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2357 0 36 30 2423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192445
X-RAY DIFFRACTIONr_bond_other_d0.0020.022248
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.9683332
X-RAY DIFFRACTIONr_angle_other_deg1.09535154
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9755299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.01224.865111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.92915392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2211510
X-RAY DIFFRACTIONr_chiral_restr0.1630.2379
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022749
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_it6.3196.9971199
X-RAY DIFFRACTIONr_mcbond_other6.3016.9961198
X-RAY DIFFRACTIONr_mcangle_it8.82610.5041497
X-RAY DIFFRACTIONr_mcangle_other8.82610.5071498
X-RAY DIFFRACTIONr_scbond_it6.7927.4311245
X-RAY DIFFRACTIONr_scbond_other6.7977.4271243
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.00410.9361836
X-RAY DIFFRACTIONr_long_range_B_refined13.0166.53410424
X-RAY DIFFRACTIONr_long_range_B_other13.01166.55310412
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.651→2.72 Å
RfactorNum. reflection% reflection
Rfree0.346 67 -
Rwork0.35 1105 -
obs--99.24 %

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