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- PDB-6w6b: The X-ray crystal structure of the C-terminus domain of Staphyloc... -

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Basic information

Entry
Database: PDB / ID: 6w6b
TitleThe X-ray crystal structure of the C-terminus domain of Staphylococcus aureus Fatty Acid Kinase A (FakA, residues 328-548) protein to 1.40 Angstrom resolution
ComponentsSaFakA-Cterminus domain
KeywordsTRANSFERASE / Fatty acid kinase A / phosphorylation / fatty acid / C-terminus domain / LIGASE
Function / homology
Function and homology information


glycerone kinase activity / glycerol metabolic process
Similarity search - Function
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
DAK2 domain-containing protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsCuypers, M.G. / Subramanian, C. / Rock, C.O. / White, S.W.
CitationJournal: To Be Published
Title: The X-ray crystal structure of the C-terminus domain of Staphylococcus aureus Fatty Acid Kinase A (FakA, residues 328-548) protein to 1.40 Angstrom resolution
Authors: Cuypers, M.G. / Subramanian, C. / Rock, C.O. / White, S.W.
History
DepositionMar 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SaFakA-Cterminus domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,42612
Polymers26,3701
Non-polymers1,05711
Water7,296405
1
A: SaFakA-Cterminus domain
hetero molecules

A: SaFakA-Cterminus domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,85324
Polymers52,7392
Non-polymers2,11322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area5120 Å2
ΔGint-239 kcal/mol
Surface area22760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.303, 87.303, 85.562
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-605-

SO4

21A-1050-

HOH

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Components

#1: Protein SaFakA-Cterminus domain / DAK2 domain-containing protein


Mass: 26369.564 Da / Num. of mol.: 1
Fragment: C-terminus domain of Safaka (residues 328-548) only in this structure
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: C7P97_10220, CSC83_01045, CSC87_04070 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S6DS72
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 405 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.7 Å3/Da / Density % sol: 66.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 1.0M Li2SO4, 1.4M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→75.61 Å / Num. obs: 71679 / % possible obs: 96.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 17.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.018 / Rrim(I) all: 0.045 / Χ2: 0.92 / Net I/σ(I): 18.8
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.972 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3645 / CC1/2: 0.754 / Rpim(I) all: 0.414 / Rrim(I) all: 1.06 / Χ2: 0.85 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimless7.0.078data scaling
HKL2Map0.4.e-betaphasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→75.61 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.366 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1487 3512 4.9 %RANDOM
Rwork0.1188 ---
obs0.1203 68164 96.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 168.41 Å2 / Biso mean: 27.098 Å2 / Biso min: 13.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.03 Å20 Å2
2--0.07 Å2-0 Å2
3----0.22 Å2
Refinement stepCycle: final / Resolution: 1.4→75.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1771 0 55 407 2233
Biso mean--80.98 49.35 -
Num. residues----233
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0131920
X-RAY DIFFRACTIONr_bond_other_d0.0070.0171731
X-RAY DIFFRACTIONr_angle_refined_deg2.2161.6272620
X-RAY DIFFRACTIONr_angle_other_deg1.7041.5714066
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8415249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8327.22983
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.17115346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg32.912152
X-RAY DIFFRACTIONr_chiral_restr0.1380.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022135
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02311
X-RAY DIFFRACTIONr_rigid_bond_restr15.31433650
LS refinement shellResolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 251 -
Rwork0.211 5160 -
all-5411 -
obs--99.34 %

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