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

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Basic information

Entry
Database: PDB / ID: 6ebv
TitleStaphylococcus aureus Type II pantothenate kinase in complex with ADP and pantothenate analog Deoxy-N7-Pan
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
Chem-27Q / ADENOSINE-5'-DIPHOSPHATE / Type II pantothenate kinase / Type II pantothenate kinase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsChen, Y. / Antoshchenko, T. / Strauss, E. / Barnard, L. / Huang, Y.H. / Park, 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
DepositionAug 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: 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)119,80212
Polymers116,5084
Non-polymers3,2948
Water61334
1
A: Type II pantothenate kinase
C: Type II pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9016
Polymers58,2542
Non-polymers1,6474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7010 Å2
ΔGint-59 kcal/mol
Surface area20800 Å2
MethodPISA
2
B: Type II pantothenate kinase
D: Type II pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9016
Polymers58,2542
Non-polymers1,6474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7040 Å2
ΔGint-57 kcal/mol
Surface area20820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.800, 56.720, 133.620
Angle α, β, γ (deg.)90.000, 99.810, 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: 29126.949 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: coaW, BTN44_13005, C3B39_13135, EP54_10775, EQ90_06670, 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-27Q / N-heptyl-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide


Mass: 396.416 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H33N2O7P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.33 Å3/Da / Density % sol: 47.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M lithium sulfate, 0.1 M Tris, pH 8.5, 33% PEG4000, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.62 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 16, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.62 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 21357 / % possible obs: 97.5 % / Redundancy: 2.81 % / Net I/σ(I): 5.82
Reflection shellResolution: 3→3.18 Å / Redundancy: 2.79 % / Mean I/σ(I) obs: 2.14 / Num. unique obs: 3421 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMACrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
SCALAdata scaling
BUSTERphasing
RefinementResolution: 3→44.49 Å / Cor.coef. Fo:Fc: 0.791 / Cor.coef. Fo:Fc free: 0.76 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.512
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1046 4.9 %RANDOM
Rwork0.228 ---
obs0.231 21348 97.5 %-
Displacement parametersBiso max: 128.36 Å2 / Biso mean: 42.7 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--29.408 Å20 Å228.1603 Å2
2--19.6429 Å20 Å2
3---9.7652 Å2
Refine analyzeLuzzati coordinate error obs: 0.47 Å
Refinement stepCycle: final / Resolution: 3→44.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8123 0 204 34 8361
Biso mean--39.13 14.71 -
Num. residues----1064
LS refinement shellResolution: 3→3.15 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.334 143 5.11 %
Rwork0.248 2657 -
all0.252 2800 -
obs--96.82 %

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