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

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Basic information

Entry
Database: PDB / ID: 6awh
TitleStaphylococcus aureus Type II pantothenate kinase in complex with ATP and pantothenate analog Deoxy-MeO-N5Pan
ComponentsType II pantothenate kinase
KeywordsTRANSFERASE / Staphylococcus aureus / SaPanK / ATP / 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'-TRIPHOSPHATE / Chem-N7G / Type II pantothenate kinase / Type II pantothenate kinase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)119,32716
Polymers115,9914
Non-polymers3,33612
Water11,440635
1
A: Type II pantothenate kinase
B: Type II pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6638
Polymers57,9962
Non-polymers1,6686
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7290 Å2
ΔGint-66 kcal/mol
Surface area20520 Å2
MethodPISA
2
C: Type II pantothenate kinase
D: Type II pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6638
Polymers57,9962
Non-polymers1,6686
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7290 Å2
ΔGint-66 kcal/mol
Surface area20530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.776, 136.671, 141.393
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-N7G / (2R)-2-hydroxy-N-{3-[(5-methoxypentyl)amino]-3-oxopropyl}-3,3-dimethylbutanamide


Mass: 302.410 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H30N2O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 635 / 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: 2.36 Å3/Da / Density % sol: 47.99 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 23% PEG3350, 0.1 M ammonium sulfate, 0.1 M Bis-Tris, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 17, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→98.27 Å / Num. obs: 87345 / % possible obs: 99.4 % / Redundancy: 5.56 % / Net I/σ(I): 4.9
Reflection shellHighest resolution: 1.9 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→98.27 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.494 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.144
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2256 4363 5 %RANDOM
Rwork0.1949 ---
obs0.1964 82792 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 104.71 Å2 / Biso mean: 29.326 Å2 / Biso min: 12.92 Å2
Baniso -1Baniso -2Baniso -3
1--1.82 Å2-0 Å20 Å2
2--3 Å2-0 Å2
3----1.18 Å2
Refinement stepCycle: final / Resolution: 1.9→98.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8121 0 212 635 8968
Biso mean--21.82 34.02 -
Num. residues----1059
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0198483
X-RAY DIFFRACTIONr_bond_other_d0.0080.028118
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.97311514
X-RAY DIFFRACTIONr_angle_other_deg1.8223.00518606
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.43351055
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.50325.286384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.612151389
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0881532
X-RAY DIFFRACTIONr_chiral_restr0.0920.21308
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029675
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021943
LS refinement shellResolution: 1.898→1.947 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 317 -
Rwork0.345 5770 -
all-6087 -
obs--95.32 %

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