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

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Basic information

Entry
Database: PDB / ID: 8vip
TitleCrystal structure of the N-terminal domain of fatty acid kinase A (FakA) from Staphylococcus aureus (Mn and AMP-PNP)
ComponentsFATTY ACID KINASE A
KeywordsLIGASE / Fatty Acid Kinase A / 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 / SAD / Resolution: 1.77 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)25,4324
Polymers24,8161
Non-polymers6163
Water2,576143
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)42.812, 57.025, 81.696
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
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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.01 Å3/Da / Density % sol: 38.78 %
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 MnCl2 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 MnCl2 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: 1.7712 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: 1.7712 Å / Relative weight: 1
ReflectionResolution: 1.77→46.76 Å / Num. obs: 36210 / % possible obs: 97.2 % / Redundancy: 10.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.02 / Rrim(I) all: 0.068 / Χ2: 0.91 / Net I/σ(I): 24.2
Reflection shellResolution: 1.77→1.81 Å / % possible obs: 72.5 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.335 / Num. measured all: 2095 / Num. unique obs: 798 / CC1/2: 0.884 / Rpim(I) all: 0.22 / Rrim(I) all: 0.404 / Χ2: 0.82 / Net I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
PHENIX(1.15_3460: ???)refinement
Aimlessdata scaling
XDSdata reduction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.77→46.76 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0.09 / Phase error: 18.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1861 1756 4.85 %
Rwork0.1481 --
obs0.1499 36210 96.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.77→46.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1536 0 33 143 1712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091582
X-RAY DIFFRACTIONf_angle_d1.0922143
X-RAY DIFFRACTIONf_dihedral_angle_d11.303957
X-RAY DIFFRACTIONf_chiral_restr0.061257
X-RAY DIFFRACTIONf_plane_restr0.006275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7701-1.8180.2708770.21221817X-RAY DIFFRACTION66
1.818-1.87150.20451270.18692553X-RAY DIFFRACTION92
1.8715-1.93190.1991370.16692664X-RAY DIFFRACTION97
1.9319-2.00090.24361130.15312711X-RAY DIFFRACTION98
2.0009-2.08110.18881480.14292714X-RAY DIFFRACTION99
2.0811-2.17580.17491560.13562706X-RAY DIFFRACTION99
2.1758-2.29050.18371490.13582767X-RAY DIFFRACTION100
2.2905-2.4340.19081390.13422737X-RAY DIFFRACTION100
2.434-2.62190.18161210.12922789X-RAY DIFFRACTION100
2.6219-2.88570.19131610.14522732X-RAY DIFFRACTION100
2.8857-3.30320.1641300.15372770X-RAY DIFFRACTION100
3.3032-4.16130.19591660.13732727X-RAY DIFFRACTION100
4.1613-46.760.16771320.16482767X-RAY DIFFRACTION100

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