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- PDB-5elz: Staphylococcus aureus Type II pantothenate kinase in complex with... -

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Basic information

Entry
Database: PDB / ID: 5elz
TitleStaphylococcus aureus Type II pantothenate kinase in complex with a pantothenate analog
ComponentsType II pantothenate kinase
KeywordsTransferase/Transferase Inhibitor / Pantothenate kinase / Structural Genomics / Structural Genomics Consortium / SGC / Transferase-Transferase Inhibitor complex
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-3V9 / ADENOSINE-5'-DIPHOSPHATE / Type II pantothenate kinase / Type II pantothenate kinase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMottaghi, K. / Hughes, S.J. / Tempel, W. / Hong, B. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: Acs Infect Dis. / Year: 2016
Title: Discovery of Potent Pantothenamide Inhibitors of Staphylococcus aureus Pantothenate Kinase through a Minimal SAR Study: Inhibition Is Due to Trapping of the Product.
Authors: Hughes, S.J. / Barnard, L. / Mottaghi, K. / Tempel, W. / Antoshchenko, T. / Hong, B.S. / Allali-Hassani, A. / Smil, D. / Vedadi, M. / Strauss, E. / Park, H.W.
History
DepositionNov 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type II pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8406
Polymers29,9561
Non-polymers8845
Water4,954275
1
A: Type II pantothenate kinase
hetero molecules

A: Type II pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,67912
Polymers59,9122
Non-polymers1,76810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area7140 Å2
ΔGint-78 kcal/mol
Surface area22680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.967, 136.771, 73.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-634-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 29955.818 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MW2 / Gene: coaW, MW2054 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-TR
References: UniProt: Q8NVG0, UniProt: Q2FWC7*PLUS, pantothenate kinase

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Non-polymers , 5 types, 280 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-3V9 / N-(1,3-benzodioxol-5-ylmethyl)-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide


Mass: 432.362 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H25N2O9P
#5: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.4 Å3/Da / Density % sol: 48.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8.5
Details: 0.5 ul protein + 0.5 uL buffer that contains 25% PEG3350, 0.2 M MgCl2, 0.1 M Tris HCl, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Mar 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→28.48 Å / Num. obs: 27062 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 23.1
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 4 / % possible all: 99.2

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Processing

Software
NameVersionClassification
XDSdata reduction
REFMAC5.7.0032refinement
SCALAdata scaling
Cootmodel building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4M7X

4m7x


Resolution: 1.8→28 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.1936 / WRfactor Rwork: 0.1557 / FOM work R set: 0.8873 / SU B: 4.476 / SU ML: 0.08 / SU R Cruickshank DPI: 0.1225 / SU Rfree: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2074 1363 5 %RANDOM
Rwork0.169 25681 --
obs0.1708 25681 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.83 Å2 / Biso mean: 24.876 Å2 / Biso min: 9.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2---1.32 Å20 Å2
3---1.16 Å2
Refinement stepCycle: final / Resolution: 1.8→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2103 0 59 275 2437
Biso mean--16.81 31.28 -
Num. residues----272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192239
X-RAY DIFFRACTIONr_bond_other_d0.0030.022117
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.9613049
X-RAY DIFFRACTIONr_angle_other_deg0.7553.0044854
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4595279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.82124.953107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.08115364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.903159
X-RAY DIFFRACTIONr_chiral_restr0.1040.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022581
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02537
X-RAY DIFFRACTIONr_mcbond_it0.9251.2581098
X-RAY DIFFRACTIONr_mcbond_other0.9251.2561097
X-RAY DIFFRACTIONr_mcangle_it1.6061.8811374
LS refinement shellResolution: 1.8→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 100 -
Rwork0.279 1815 -
all-1915 -
obs--98.21 %
Refinement TLS params.Method: refined / Origin x: 17.2881 Å / Origin y: 14.3542 Å / Origin z: -3.5316 Å
111213212223313233
T0.0209 Å20.0013 Å2-0.0017 Å2-0.0379 Å20.0018 Å2--0.0422 Å2
L1.2047 °2-0.2599 °2-0.1082 °2-2.439 °20.2347 °2--0.7962 °2
S0.0646 Å °0.0112 Å °0.2001 Å °-0.1377 Å °-0.1125 Å °0.0546 Å °-0.1048 Å °-0.0149 Å °0.0479 Å °

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