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- PDB-4m7y: Staphylococcus aureus Type II pantothenate kinase in complex with... -

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Basic information

Entry
Database: PDB / ID: 4m7y
TitleStaphylococcus aureus Type II pantothenate kinase in complex with a pantothenate analog
ComponentsType II pantothenate kinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / pantothenate kinase / inhibitor / antibacterial / 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-2GH / ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Type II pantothenate kinase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsMottaghi, K. / Hong, B. / Tempel, W. / 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
DepositionAug 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Dec 28, 2016Group: Database references
Revision 1.3Sep 20, 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 / diffrn_source / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.type / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,16835
Polymers59,9122
Non-polymers2,25633
Water3,477193
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8420 Å2
ΔGint-111 kcal/mol
Surface area19740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.960, 56.130, 68.420
Angle α, β, γ (deg.)90.000, 101.170, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-458-

HOH

DetailsAS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 29955.818 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: MW2 / Gene: coaW, MW2054 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-TR / References: UniProt: Q8NVG0, pantothenate kinase

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Non-polymers , 5 types, 226 molecules

#2: Chemical ChemComp-2GH / N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-pentyl-beta-alaninamide


Mass: 368.363 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H29N2O7P
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#5: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 22 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.3 Å3/Da / Density % sol: 46.3 %
Crystal growMethod: vapor diffusion / pH: 7
Details: 0.01 M inhibitor, 0.01 M magnesium chloride, 0.01 M ATP were added to the protein sample. Crystal condition: 2.5 M ammonium sulfate, 0.1 M BTP, 1.1 % w/v Cyclohexylethanoyl-N- ...Details: 0.01 M inhibitor, 0.01 M magnesium chloride, 0.01 M ATP were added to the protein sample. Crystal condition: 2.5 M ammonium sulfate, 0.1 M BTP, 1.1 % w/v Cyclohexylethanoyl-N-hydroxyethylglucamide., pH 7.0, vapor diffusion

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Mar 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 48878 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 33.94 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.87
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.8-1.850.95225407358999
1.85-1.90.7582.5924444349899.3
1.9-1.950.6053.323768339999.1
1.95-2.010.4624.2223250332099.2
2.01-2.080.3115.8622804318299.7
2.08-2.150.2676.8322363313299.9
2.15-2.230.2417.8620919298699.5
2.23-2.320.1919.8920542290699.4
2.32-2.430.15411.4619692276799.9
2.43-2.550.13412.9419448269099.5
2.55-2.680.10715.9817613251299.1
2.68-2.850.08619.7117422239899.8
2.85-3.040.07622.6915263220598.7
3.04-3.290.05929.0114715211699.1
3.29-3.60.0534.9313967194299.9
3.6-4.030.04538.4912611177499.2
4.03-4.650.03942.0110495152699
4.65-5.690.03841.539436132199.5
5.69-8.050.03642.447499104199.8
8.050.02749.88397657496.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.7.0027refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4m7x

4m7x


Resolution: 1.8→26.532 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.208 / WRfactor Rwork: 0.167 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 6.661 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED. INHIBITOR RESTRAINTS WERE BASED ON PRODRG CALCULATIONS. COOT AND THE MOLPROBITY SERVER WERE ALSO USED DURING ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED. INHIBITOR RESTRAINTS WERE BASED ON PRODRG CALCULATIONS. COOT AND THE MOLPROBITY SERVER WERE ALSO USED DURING REFINEMENT. SOME DUMMY ATOMS AND PHOSPHATE IONS B303, B304, A303, B305 OF THE MODEL REPRESENT ELECTRON DENSITY THAT APPEARS TO ARISE FROM A LARGER, UNIDENTIFIED MOLECULE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2198 2074 4.25 %thin shells (sftools)
Rwork0.1761 ---
obs0.178 48796 99.227 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso max: 83.01 Å2 / Biso mean: 31.734 Å2 / Biso min: 15.15 Å2
Baniso -1Baniso -2Baniso -3
1-2.136 Å20 Å2-0.599 Å2
2---0.646 Å20 Å2
3----1.721 Å2
Refinement stepCycle: LAST / Resolution: 1.8→26.532 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3950 0 159 193 4302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.024282
X-RAY DIFFRACTIONr_bond_other_d0.0020.023975
X-RAY DIFFRACTIONr_angle_refined_deg1.5411.9765863
X-RAY DIFFRACTIONr_angle_other_deg0.7513.0029025
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4365559
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.49924.696181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.43415647
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7751517
X-RAY DIFFRACTIONr_chiral_restr0.0760.2678
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024923
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02988
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.8470.2924210.2713153360799.085
1.847-1.89700.2743484351199.231
1.897-1.95200.2563364340198.912
1.952-2.0110.2833340.2212975333499.25
2.011-2.07700.1853182319799.531
2.077-2.1490.2591250.1762960309699.645
2.149-2.230.2262080.1782781300499.501
2.23-2.3200.1722896291499.382
2.32-2.4230.2182550.1672490276099.457
2.423-2.5400.1772675268899.516
2.54-2.6760.2132000.1732289252398.652
2.676-2.83600.182399240599.751
2.836-3.030.2591550.1922058224298.707
3.03-3.26900.1872097212598.682
3.269-3.5750.1981130.1651827194699.692
3.575-3.9880.1721180.1431645177699.268
3.988-4.5880.153600.121491157398.601
4.588-5.5780.121100.1521319133799.402
5.578-7.720.263560.1951005106399.812
7.72-26.5320.216190.17663265499.541
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.91660.16740.40131.23650.51532.9544-0.0312-0.1160.02860.13030.0125-0.06260.02480.10870.01870.02070.00830.00540.02420.00010.0522-16.177522.46-23.9676
21.13250.43440.3891.89680.92792.2046-0.01160.1354-0.1072-0.07740.1197-0.19990.27430.3818-0.1080.08530.05070.04530.1007-0.02490.0801-10.20877.9957-46.8829
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 266
2X-RAY DIFFRACTION1A301 - 302
3X-RAY DIFFRACTION2B1 - 266
4X-RAY DIFFRACTION2B301 - 302

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