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- PDB-7uq1: The X-ray crystal structure of the N-terminal domain of Staphyloc... -

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Basic information

Entry
Database: PDB / ID: 7uq1
TitleThe X-ray crystal structure of the N-terminal domain of Staphylococcus aureus Fatty Acid Kinase A (FakA, residues 1-208) in complex with AMP and a single Mg ion at the dinuclear binding site
ComponentsFatty Acid Kinase A
KeywordsLIGASE / Fatty acid kinase A / phosphorylation / fatty acid / N-terminus domain
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 / DhaL domain superfamily / DAK2 domain ...: / 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 / DhaL domain superfamily / DAK2 domain / DhaL domain profile. / Dak2 / : / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Uncharacterized protein SA1069
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsCuypers, M.G. / Subramanian, C. / Seetharaman, J. / Rock, C.O. / White, S.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Domain architecture and catalysis of the Staphylococcus aureus fatty acid kinase.
Authors: Subramanian, C. / Cuypers, M.G. / Radka, C.D. / White, S.W. / Rock, C.O.
History
DepositionApr 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fatty Acid Kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9586
Polymers24,4461
Non-polymers5125
Water3,477193
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.843, 54.289, 81.824
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Fatty Acid Kinase A


Mass: 24445.777 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7A5Z4
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.9 Å3/Da / Density % sol: 35.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2M MgCl2, 0.1M Tris HCl pH8.5, 30%PEG4000, (JCSG Core IV #21)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.72→29.25 Å / Num. obs: 20367 / % possible obs: 99.7 % / Redundancy: 5.4 % / Biso Wilson estimate: 23.27 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.061 / Net I/σ(I): 6.1
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.6 / Num. unique obs: 1077 / CC1/2: 0.79 / Rpim(I) all: 0.304 / Χ2: 0.25 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7SNB

7snb


Resolution: 1.72→29.25 Å / SU ML: 0.1997 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.0867
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.223 963 4.74 %
Rwork0.1739 19359 -
obs0.1762 20322 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.67 Å2
Refinement stepCycle: LAST / Resolution: 1.72→29.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1565 0 32 193 1790
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00341609
X-RAY DIFFRACTIONf_angle_d0.66732169
X-RAY DIFFRACTIONf_chiral_restr0.041255
X-RAY DIFFRACTIONf_plane_restr0.0037279
X-RAY DIFFRACTIONf_dihedral_angle_d8.9252228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.810.33771350.27562733X-RAY DIFFRACTION99.86
1.81-1.920.28551230.22642727X-RAY DIFFRACTION99.86
1.92-2.070.24231350.18732742X-RAY DIFFRACTION99.9
2.07-2.280.23851180.17072775X-RAY DIFFRACTION99.93
2.28-2.610.24131560.16682741X-RAY DIFFRACTION99.69
2.61-3.290.21661430.17532770X-RAY DIFFRACTION99.05
3.29-29.250.1941530.15562871X-RAY DIFFRACTION97.96
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)
17.524034173122.864152497145.918582134758.169309473973.77378504824.998286637940.164161387342-0.8273593287710.1734165986210.7252170315710.0686752157613-0.355105538239-0.1505713402041.24799898673-0.3577593453940.460067741184-0.07354995755390.01723987812340.896669204086-0.1020565361010.256023211561-3.20607657346-2.1833986264630.8360024678
21.996707801090.83310596324-1.29868467860.547623371406-0.7223160846277.66378786180.07551312371660.06474599195730.3713675284590.05215320894260.03620782797680.126203950587-0.409001490532-0.116468767471-0.10447364260.245731607950.052266932157-0.005407660966020.205692481895-0.01284698156880.236884213279-13.61487897750.6813491645147.38069172401
32.06406591214-0.0338511663153-2.13376651922.814371711512.501592628184.364337563060.171123012358-0.360732752888-0.2397770394390.23783884839-0.01999016226410.347732170250.00120967965874-0.432794756370.1250245060370.2013907100810.04062926977840.06184255842320.312392930497-0.02119322303260.193551969879-19.6732390994-8.8552581852717.2804366181
43.58761555434-1.182891103822.914309232755.06950662125-3.322848042415.08528170832-0.0549031826955-0.2377969271440.05527983145540.156644270703-0.0146420933858-0.0275292595489-0.253202110906-0.1391876224160.06358151778780.1344669871960.01654539267990.02169609051620.196573246004-0.02357756785480.15204780097-11.7878101927-12.086876090810.1749051594
53.621404750562.0917270618-2.932340413588.515398602540.03167786376985.29275597898-0.219445079138-1.19787009686-1.070642670730.955881314445-0.0940097424203-0.3555046872351.160917207530.08509037607550.0698094291220.5296815701210.0397051771080.03715822759110.4185038007640.07802337596440.329419806925-10.0508030159-13.846528122726.928712072
63.038429586451.308211315441.487823925442.572648735191.350319645876.397622965320.0552932625359-0.30804656665-0.2234100395260.147944935459-0.0139645562151-0.04480017816350.4638025349510.0617794491504-0.1021747068690.1519276012050.0506360935280.003508162863840.2086226803260.02640631690170.194960624203-4.05131706253-14.85625588288.81983229423
73.51270393615-0.2905910550822.567430525454.376666914181.22392342787.280962095050.198912358749-0.389453861913-0.1963582076880.5017236280990.0638245360976-0.4519758368170.7683998869040.875719663891-0.2580597147320.2230798728520.00765849546311-0.007288855791170.3934240200160.0190798125510.2503808169383.46664595202-9.2872000649315.372597365
82.52474475286-0.379126045265-2.248969684121.14424433671.135418738495.379607693860.188849888357-0.4043065227090.3835095537740.1123362357340.0753788389663-0.0984139410413-0.3394688889350.617712233913-0.3168359206580.288035685423-0.0422593066001-0.01298522912630.3112473471-0.05382114972990.2914030082284.12585511994-2.0952906784911.1291030689
96.42710046561-2.08308737845-0.1184590436512.96400670535-3.672175460086.954991103290.4422632410530.646618730880.464041561641-0.11150088911-0.4183301099010.00344948963871-0.5398723938010.1484093246530.05754546281420.3323416799490.03183307216110.01118465068270.3348057062630.05819959557130.2649509111681.81171613479-1.63531325714-7.25830026086
102.400373462420.365644051378-0.2354607949271.053610103282.189635530926.71971511530.454902579748-0.5159520570141.015778151910.0929219839820.02375026503370.013854772436-1.464225613840.1879386117320.544014315660.345044706019-0.05052960488030.05501993186830.280668875661-0.1068532303850.251602012578-6.029314090352.5066345501914.4290490277
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid -2 through 6 )-2 - 61 - 9
22chain 'A' and (resid 7 through 57 )7 - 5710 - 60
33chain 'A' and (resid 58 through 80 )58 - 8061 - 83
44chain 'A' and (resid 81 through 98 )81 - 9884 - 101
55chain 'A' and (resid 99 through 105 )99 - 105102 - 108
66chain 'A' and (resid 106 through 131 )106 - 131109 - 134
77chain 'A' and (resid 132 through 152 )132 - 152135 - 155
88chain 'A' and (resid 153 through 173 )153 - 173156 - 176
99chain 'A' and (resid 174 through 185 )174 - 185177 - 188
1010chain 'A' and (resid 186 through 207 )186 - 207189 - 210

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