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- PDB-6b9i: The crystal structure of the Staphylococcus aureus Fatty acid Kin... -

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Basic information

Entry
Database: PDB / ID: 6b9i
TitleThe crystal structure of the Staphylococcus aureus Fatty acid Kinase (Fak) B1 protein loaded with 14-Methylhexadecanoic Acid (Anteiso C17:0) to 1.93 Angstrom resolution
ComponentsFatty acid Kinase (Fak) B1
KeywordsTRANSFERASE / Staphylococcus aureus / FakB1 / 12-Methyl 14-Methylhexadecanoic / anteiso C17:0
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
(14S)-14-methylhexadecanoic acid / DegV domain-containing protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsCuypers, M.G. / Ericson, M. / Subramanian, C. / White, S.W. / Rock, C.O.
CitationJournal: J. Biol. Chem. / Year: 2019
Title: Acyl-chain selectivity and physiological roles ofStaphylococcus aureusfatty acid-binding proteins.
Authors: Cuypers, M.G. / Subramanian, C. / Gullett, J.M. / Frank, M.W. / White, S.W. / Rock, C.O.
History
DepositionOct 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity / Item: _citation.title / _entity.formula_weight
Revision 1.2Nov 28, 2018Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Jan 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.4Oct 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: Fatty acid Kinase (Fak) B1
B: Fatty acid Kinase (Fak) B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,80317
Polymers64,2032
Non-polymers1,60015
Water7,963442
1
A: Fatty acid Kinase (Fak) B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0179
Polymers32,1021
Non-polymers9158
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fatty acid Kinase (Fak) B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7868
Polymers32,1021
Non-polymers6857
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.991, 54.170, 83.901
Angle α, β, γ (deg.)104.71, 90.00, 107.73
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Fatty acid Kinase (Fak) B1 / EDD / DegV family domain protein / Fatty acid-binding protein DegV


Mass: 32101.506 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: AYM28_04055, AYM37_04055, ERS072738_00223, ERS072840_01626, ERS074020_00218, HMPREF3211_01094
Production host: Escherichia coli (E. coli) / References: UniProt: X5EH37
#2: Chemical ChemComp-D0G / (14S)-14-methylhexadecanoic acid


Mass: 270.451 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H34O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 2.14 Å3/Da / Density % sol: 42.63 %
Crystal growTemperature: 295 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→80.87 Å / Num. obs: 39271 / % possible obs: 97.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 16.73 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.08 / Rrim(I) all: 0.157 / Net I/σ(I): 10.1
Reflection shellResolution: 1.93→1.98 Å / Redundancy: 2 % / Rmerge(I) obs: 0.629 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2578 / Rpim(I) all: 0.592 / Rrim(I) all: 0.866 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX(dev_2906: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UTO

5uto


Resolution: 1.93→38.073 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 22.27
RfactorNum. reflection% reflection
Rfree0.2064 1937 4.93 %
Rwork0.1663 --
obs0.1683 39257 97.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.93→38.073 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4392 0 106 442 4940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034626
X-RAY DIFFRACTIONf_angle_d0.556227
X-RAY DIFFRACTIONf_dihedral_angle_d17.891748
X-RAY DIFFRACTIONf_chiral_restr0.046692
X-RAY DIFFRACTIONf_plane_restr0.003797
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.97830.32671320.26652591X-RAY DIFFRACTION96
1.9783-2.03180.30781550.22542629X-RAY DIFFRACTION97
2.0318-2.09150.26071470.19252666X-RAY DIFFRACTION97
2.0915-2.1590.19121410.17972636X-RAY DIFFRACTION97
2.159-2.23620.22151590.16492605X-RAY DIFFRACTION97
2.2362-2.32570.20691190.16632670X-RAY DIFFRACTION97
2.3257-2.43150.22891260.17072698X-RAY DIFFRACTION98
2.4315-2.55970.27321260.17142685X-RAY DIFFRACTION98
2.5597-2.720.2321020.17192706X-RAY DIFFRACTION98
2.72-2.930.20221110.16572673X-RAY DIFFRACTION99
2.93-3.22470.19441530.15842703X-RAY DIFFRACTION99
3.2247-3.6910.17021540.14192673X-RAY DIFFRACTION99
3.691-4.6490.15611420.13912703X-RAY DIFFRACTION99
4.649-38.08080.19691700.16482682X-RAY DIFFRACTION100

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