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- PDB-6awi: Staphylococcus aureus Type II pantothenate kinase in complex with... -

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Basic information

Entry
Database: PDB / ID: 6awi
TitleStaphylococcus aureus Type II pantothenate kinase in complex with ADP and pantothenate analog Deoxy-N5Pan
ComponentsType II pantothenate kinase
KeywordsTRANSFERASE / Staphylococcus aureus / SaPanK / ADP / pantothenate analog
Function / homology
Function and homology information


pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / ATP binding / cytosol
Similarity search - Function
Type II pantothenate kinase, bacterial / Fumble / Type II pantothenate kinase / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-C0D / Type II pantothenate kinase / Type II pantothenate kinase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChen, Y. / Antoshchenko, T. / Strauss, E. / Barnard, L. / Huang, Y.H.
CitationJournal: To Be Published
Title: Structure-based identification of uncompetitive inhibitors for Staphylococcus aureus pantothenate kinase.
Authors: Chen, Y. / Antoshchenko, T. / Strauss, E. / Barnard, L. / Huang, Y.H.
History
DepositionSep 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
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: Type II pantothenate kinase
B: Type II pantothenate kinase
C: Type II pantothenate kinase
D: Type II pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,78912
Polymers115,9914
Non-polymers2,7988
Water9,908550
1
A: Type II pantothenate kinase
B: Type II pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3956
Polymers57,9962
Non-polymers1,3994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-56 kcal/mol
Surface area20920 Å2
MethodPISA
2
C: Type II pantothenate kinase
D: Type II pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3956
Polymers57,9962
Non-polymers1,3994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-55 kcal/mol
Surface area21020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.388, 57.042, 134.077
Angle α, β, γ (deg.)90.000, 99.880, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Type II pantothenate kinase / PanK-II / Pantothenic acid kinase


Mass: 28997.770 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: coaW, AYM28_11860, AYM37_11860, ERS072738_01917, ERS074020_01878, HMPREF3211_02599
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0D6HHM8, UniProt: Q2FWC7*PLUS, pantothenate kinase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-C0D / (2R)-2-hydroxy-3,3-dimethyl-N-[3-oxo-3-(pentylamino)propyl]butanamide


Mass: 272.384 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H28N2O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 550 / 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: 2.38 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG4000, 0.2 M lithium sulfate, 0.1 M Tris-HCl, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 30, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.8→132.09 Å / Num. obs: 101733 / % possible obs: 99.6 % / Redundancy: 4.46 % / Net I/σ(I): 10.91
Reflection shellHighest resolution: 1.8 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.722 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.13
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2333 4985 4.9 %RANDOM
Rwork0.1883 ---
obs0.1905 96433 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 92.85 Å2 / Biso mean: 28.973 Å2 / Biso min: 9.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.85 Å2-0 Å2-1.99 Å2
2---0.91 Å20 Å2
3----0.23 Å2
Refinement stepCycle: final / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8155 0 184 550 8889
Biso mean--21.89 31.8 -
Num. residues----1063
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0198483
X-RAY DIFFRACTIONr_bond_other_d0.0060.028128
X-RAY DIFFRACTIONr_angle_refined_deg1.8961.9711512
X-RAY DIFFRACTIONr_angle_other_deg1.0083.00418628
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.59351059
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.64725.349387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.185151394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7381532
X-RAY DIFFRACTIONr_chiral_restr0.120.21311
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029719
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021949
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 351 -
Rwork0.32 7108 -
all-7459 -
obs--99.39 %

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