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- PDB-5uto: The crystal structure of the Staphylococcus aureus Fatty acid Kin... -

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Basic information

Entry
Database: PDB / ID: 5uto
TitleThe crystal structure of the Staphylococcus aureus Fatty acid Kinase (Fak) B1 protein loaded with palmitic acid to 1.83 Angstrom resolution
ComponentsEDD domain protein, DegV family
KeywordsTRANSPORT PROTEIN / Staphylococcus aureus / FakB1 / palmitic acid
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
PALMITIC ACID / DegV domain-containing protein / DegV domain-containing protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsCuypers, M.G. / Ericson, M. / Subramanian, C. / Broussard, T.C. / Miller, D.J. / White, S.W. / Rock, C.O.
CitationJournal: J.Biol.Chem. / Year: 2018
Title: The crystal structure of the Staphylococcus aureus Fatty acid Kinase (Fak) B1 protein loaded with palmitic acid to 1.83 Angstroem resolution
Authors: Cuypers, M.G. / Ericson, M. / Subramanian, C. / Broussard, T.C. / Miller, D.J. / White, S.W. / Rock, C.O.
History
DepositionFeb 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.year
Revision 1.2Oct 4, 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

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Assembly

Deposited unit
A: EDD domain protein, DegV family
B: EDD domain protein, DegV family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0594
Polymers68,5462
Non-polymers5132
Water11,512639
1
A: EDD domain protein, DegV family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5292
Polymers34,2731
Non-polymers2561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: EDD domain protein, DegV family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5292
Polymers34,2731
Non-polymers2561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.191, 54.289, 84.396
Angle α, β, γ (deg.)105.18, 90.02, 107.50
Int Tables number1
Space group name H-MP1

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Components

#1: Protein EDD domain protein, DegV family / EDD / DegV family domain protein


Mass: 34272.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: ERS072738_00223, ERS072840_01626, ERS074020_00218, HMPREF3211_01094
Production host: Escherichia coli (E. coli) / References: UniProt: X5EH37, UniProt: P0A0N2*PLUS
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 639 / 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: 2.17 Å3/Da / Density % sol: 43.43 % / Description: elongated prisms
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
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 temperature room

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 1, 2016 / Details: Si(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→48.83 Å / Num. obs: 46256 / % possible obs: 97.1 % / Redundancy: 3.1 % / Biso Wilson estimate: 15.21 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.046 / Rrim(I) all: 0.082 / Net I/σ(I): 12.3
Reflection shellResolution: 1.83→1.87 Å / Redundancy: 3 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2815 / CC1/2: 0.694 / Rpim(I) all: 0.443 / Rrim(I) all: 0.782 / % possible all: 95.3

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Processing

Software
NameVersionClassification
PHENIXdev_2614refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X9X

4x9x


Resolution: 1.83→38.034 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 20.11 / Details: Automated water placement.
RfactorNum. reflection% reflection
Rfree0.1911 2208 4.77 %
Rwork0.1581 --
obs0.1597 46245 97.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.83→38.034 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4498 0 36 639 5173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034746
X-RAY DIFFRACTIONf_angle_d0.546416
X-RAY DIFFRACTIONf_dihedral_angle_d3.7173954
X-RAY DIFFRACTIONf_chiral_restr0.046718
X-RAY DIFFRACTIONf_plane_restr0.003831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.86980.25041220.23392722X-RAY DIFFRACTION95
1.8698-1.91330.28611490.22682658X-RAY DIFFRACTION96
1.9133-1.96110.24711380.21642766X-RAY DIFFRACTION96
1.9611-2.01420.27851440.20772690X-RAY DIFFRACTION96
2.0142-2.07340.22971310.17392778X-RAY DIFFRACTION96
2.0734-2.14030.20221460.17552644X-RAY DIFFRACTION96
2.1403-2.21680.23151160.16162802X-RAY DIFFRACTION97
2.2168-2.30560.23241460.16812715X-RAY DIFFRACTION97
2.3056-2.41050.21781390.16062759X-RAY DIFFRACTION97
2.4105-2.53760.23811370.17322789X-RAY DIFFRACTION98
2.5376-2.69650.23061290.16152772X-RAY DIFFRACTION98
2.6965-2.90460.16171520.15652751X-RAY DIFFRACTION98
2.9046-3.19680.18221340.14982802X-RAY DIFFRACTION98
3.1968-3.65910.16911490.13332801X-RAY DIFFRACTION98
3.6591-4.60880.15241200.12442793X-RAY DIFFRACTION98
4.6088-38.04210.14061560.15182795X-RAY DIFFRACTION99

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