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- PDB-6nyu: The X-ray crystal structure of Staphylococcus aureus Fatty Acid K... -

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Basic information

Entry
Database: PDB / ID: 6nyu
TitleThe X-ray crystal structure of Staphylococcus aureus Fatty Acid Kinase (Fak) B1 F263T mutant protein to 2.18 Angstrom resolution
ComponentsDegV domain-containing protein
KeywordsTRANSFERASE / Fatty acid kinase
Function / homology
Function and homology information


kinase activity / lipid binding
Similarity search - Function
Rossmann fold - #10170 / DegV / DegV, C-terminal domain / Uncharacterised protein, DegV family COG1307 / DegV domain profile. / : / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
MYRISTIC ACID / PALMITIC ACID / DegV domain-containing protein / DegV domain-containing protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.183 Å
AuthorsCuypers, M.G. / Gullett, J.M. / Subramanian, C. / White, S.W. / Rock, C.O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: To Be Published
Title: The X-ray crystal structure of STAPHYLOCOCCUS AUREUS Fatty Acid Kinase (Fak) B1 protein F263T mutant to 2.18 Angstrom resolution
Authors: Cuypers, M.G. / Gullett, J.M. / Subramanian, C. / White, S.W. / Rock, C.O.
History
DepositionFeb 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: DegV domain-containing protein
B: DegV domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2658
Polymers64,1112
Non-polymers1,1546
Water5,386299
1
A: DegV domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6324
Polymers32,0551
Non-polymers5773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DegV domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6324
Polymers32,0551
Non-polymers5773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.846, 54.090, 83.729
Angle α, β, γ (deg.)105.05, 90.00, 107.67
Int Tables number1
Space group name H-MP1

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Components

#1: Protein DegV domain-containing protein / DegV family protein / EDD domain protein / DegV family / EDD / DegV family domain protein / Fatty ...DegV family protein / EDD domain protein / DegV family / EDD / DegV family domain protein / Fatty acid-binding protein DegV


Mass: 32055.436 Da / Num. of mol.: 2 / Mutation: F263T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: BTN44_08795, CV021_09110, EP54_02745, EQ90_03735, ERS072840_01626, HMPREF3211_01094, NCTC10654_00855, NCTC11940_00723, NCTC13131_00828, NCTC13196_00435, NCTC6133_00899, NCTC7878_03402, SAMEA1531701_00562
Production host: Escherichia coli (E. coli) / References: UniProt: X5EH37, UniProt: P0A0N2*PLUS
#2: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.13 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: PH 6.5 0.1M MES/IMIDAZOLE, 12.5% PEG1000, 12.5% PEG3350, 12.5% MPD, 0.03M NANO3, 0.03M NA2HPO4, 0.03M (NH4)2 SO4
Temp details: controlled room

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryostream - post 88K flash freezing / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→80.56 Å / Num. obs: 26506 / % possible obs: 96.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 16.5 Å2 / CC1/2: 0.973 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.08 / Rrim(I) all: 0.156 / Net I/σ(I): 11.6
Reflection shellResolution: 2.18→2.25 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 1800 / CC1/2: 0.552 / Rpim(I) all: 0.379 / Rrim(I) all: 0.548 / % possible all: 76.5

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Processing

Software
NameVersionClassification
PHENIX(dev_3354: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UTO

5uto


Resolution: 2.183→40.279 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 23.81
RfactorNum. reflection% reflection
Rfree0.2431 1304 4.92 %
Rwork0.1835 --
obs0.1863 26495 96.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.183→40.279 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4383 0 80 299 4762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0014565
X-RAY DIFFRACTIONf_angle_d0.3856147
X-RAY DIFFRACTIONf_dihedral_angle_d4.6733830
X-RAY DIFFRACTIONf_chiral_restr0.041689
X-RAY DIFFRACTIONf_plane_restr0.002788
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.183-2.27040.30411260.26082340X-RAY DIFFRACTION82
2.2704-2.37370.28211490.22772830X-RAY DIFFRACTION97
2.3737-2.49880.27651490.21292806X-RAY DIFFRACTION98
2.4988-2.65540.27481790.20422815X-RAY DIFFRACTION98
2.6554-2.86030.29011470.19482871X-RAY DIFFRACTION98
2.8603-3.14810.1991180.18482860X-RAY DIFFRACTION99
3.1481-3.60340.22591590.16752920X-RAY DIFFRACTION99
3.6034-4.53890.25451290.15172860X-RAY DIFFRACTION99
4.5389-40.28590.18631480.16512889X-RAY DIFFRACTION100

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