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- PDB-8viq: Crystal structure of the N-terminal domain of fatty acid kinase A... -

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Basic information

Entry
Database: PDB / ID: 8viq
TitleCrystal structure of the N-terminal domain of fatty acid kinase A (FakA) from Staphylococcus aureus (Mg and AMP-PNP)
ComponentsFATTY ACID KINASE A
KeywordsLIGASE / Fatty Acid Kinase A / Staphylococcus aureus / MRSA / proline isomerization / fatty acid metabolism
Function / homology
Function and homology information


glycerone kinase activity / glycerol metabolic process
Similarity search - Function
: / Fatty acid kinase subunit A-like, middle domain / DAK2 domain-containing protein YloV / Uncharacterised protein, DhaK domain / Fatty acid kinase subunit A-like, C-terminal / Dak1_2 / DhaL domain / DhaL domain superfamily / DAK2 domain / DhaL domain profile. ...: / Fatty acid kinase subunit A-like, middle domain / DAK2 domain-containing protein YloV / Uncharacterised protein, DhaK domain / Fatty acid kinase subunit A-like, C-terminal / Dak1_2 / DhaL domain / DhaL domain superfamily / DAK2 domain / DhaL domain profile. / Dak2 / :
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Uncharacterized protein SAOUHSC_01193
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsLovell, S. / Kashipathy, M.M. / Battaile, K.P. / Bose, J.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM110761 United States
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Molecular insights into the structure and function of the Staphylococcus aureus fatty acid kinase.
Authors: Myers, M.J. / Xu, Z. / Ryan, B.J. / DeMars, Z.R. / Ridder, M.J. / Johnson, D.K. / Krute, C.N. / Flynn, T.S. / Kashipathy, M.M. / Battaile, K.P. / Schnicker, N. / Lovell, S. / Freudenthal, B.D. / Bose, J.L.
History
DepositionJan 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 4, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FATTY ACID KINASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3714
Polymers24,8161
Non-polymers5553
Water4,125229
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.728, 56.433, 81.803
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FATTY ACID KINASE A


Mass: 24816.246 Da / Num. of mol.: 1 / Fragment: N-terminal domain (M1-A212)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Gene: SAOUHSC_01193 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2FZ58
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.99 Å3/Da / Density % sol: 38.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Proplex D9: 15% (w/v) PEG 6000, 100 mM MES pH 6.5, 5% (v/v) 2-methyl-2,4-pentanediol, Cryo: 85% crystallization solution and 15% (v/v) MPD, 2.5 mM MgCl2 and 2.5 mM AMP-PNP added to the ...Details: Proplex D9: 15% (w/v) PEG 6000, 100 mM MES pH 6.5, 5% (v/v) 2-methyl-2,4-pentanediol, Cryo: 85% crystallization solution and 15% (v/v) MPD, 2.5 mM MgCl2 and 2.5 mM AMP-PNP added to the protein prior to crystallization.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2019
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→46.45 Å / Num. obs: 81027 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.024 / Rrim(I) all: 0.061 / Χ2: 0.99 / Net I/σ(I): 12.8 / Num. measured all: 512550
Reflection shellResolution: 1.1→1.12 Å / % possible obs: 100 % / Redundancy: 6.2 % / Rmerge(I) obs: 1.133 / Num. measured all: 24635 / Num. unique obs: 3948 / CC1/2: 0.675 / Rpim(I) all: 0.492 / Rrim(I) all: 1.237 / Χ2: 1.02 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(1.15_3460: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→34.065 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.01 / Phase error: 12.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1417 3958 4.89 %
Rwork0.1254 --
obs0.1262 80922 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.1→34.065 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1543 0 33 229 1805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061653
X-RAY DIFFRACTIONf_angle_d0.9882253
X-RAY DIFFRACTIONf_dihedral_angle_d5.025963
X-RAY DIFFRACTIONf_chiral_restr0.067270
X-RAY DIFFRACTIONf_plane_restr0.006290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.11340.22341340.22372701X-RAY DIFFRACTION100
1.1134-1.12750.24841470.21792764X-RAY DIFFRACTION100
1.1275-1.14240.20381260.19522700X-RAY DIFFRACTION100
1.1424-1.1580.18711460.1872681X-RAY DIFFRACTION100
1.158-1.17450.1841480.17792716X-RAY DIFFRACTION100
1.1745-1.19210.20231490.16552712X-RAY DIFFRACTION100
1.1921-1.21070.16981320.14952704X-RAY DIFFRACTION100
1.2107-1.23060.1781280.14352754X-RAY DIFFRACTION100
1.2306-1.25180.15031600.1392676X-RAY DIFFRACTION100
1.2518-1.27450.14921570.13372713X-RAY DIFFRACTION100
1.2745-1.29910.15361480.12882741X-RAY DIFFRACTION100
1.2991-1.32560.13881390.12082706X-RAY DIFFRACTION100
1.3256-1.35440.15161460.11522732X-RAY DIFFRACTION100
1.3544-1.38590.13131450.11282735X-RAY DIFFRACTION100
1.3859-1.42060.10821410.10652742X-RAY DIFFRACTION100
1.4206-1.4590.11281590.09552705X-RAY DIFFRACTION100
1.459-1.50190.12221410.0952735X-RAY DIFFRACTION100
1.5019-1.55040.11461440.09582730X-RAY DIFFRACTION100
1.5504-1.60580.11951270.09252768X-RAY DIFFRACTION100
1.6058-1.67010.1111270.10122753X-RAY DIFFRACTION100
1.6701-1.74610.12321360.10512769X-RAY DIFFRACTION100
1.7461-1.83810.13461410.11342760X-RAY DIFFRACTION100
1.8381-1.95330.14551270.11732797X-RAY DIFFRACTION100
1.9533-2.10410.11851260.11442764X-RAY DIFFRACTION100
2.1041-2.31580.11981570.11732777X-RAY DIFFRACTION100
2.3158-2.65080.12281330.12152822X-RAY DIFFRACTION100
2.6508-3.33920.14941400.12992846X-RAY DIFFRACTION100
3.3392-34.0650.16321540.14032961X-RAY DIFFRACTION100

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