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- PDB-6nm1: The crystal structure of the Staphylococcus aureus Fatty acid Kin... -

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Basic information

Entry
Database: PDB / ID: 6nm1
TitleThe crystal structure of the Staphylococcus aureus Fatty acid Kinase (Fak) B1 protein A158L mutant to 2.33 Angstrom resolution exhibits a conformation change compared to the wild type form
ComponentsFatty acid Kinase (Fak) B1 protein
KeywordsTRANSFERASE / Staphylococcus aureus / FakB1 / mutant / conformation change
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 / DegV domain-containing protein / DegV domain-containing protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsCuypers, M.G. / Gullett, J.M. / Subramanian, C. / Ericson, M. / White, S.W. / Rock, C.O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)GM034496 United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Identification of structural transitions in bacterial fatty acid binding proteins that permit ligand entry and exit at membranes.
Authors: Gullett, J.M. / Cuypers, M.G. / Grace, C.R. / Pant, S. / Subramanian, C. / Tajkhorshid, E. / Rock, C.O. / White, S.W.
History
DepositionJan 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fatty acid Kinase (Fak) B1 protein
B: Fatty acid Kinase (Fak) B1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7444
Polymers64,2872
Non-polymers4572
Water2,414134
1
A: Fatty acid Kinase (Fak) B1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3722
Polymers32,1441
Non-polymers2281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fatty acid Kinase (Fak) B1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3722
Polymers32,1441
Non-polymers2281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.355, 53.517, 86.152
Angle α, β, γ (deg.)76.88, 89.36, 72.27
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Fatty acid Kinase (Fak) B1 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: 32143.584 Da / Num. of mol.: 2 / Mutation: A158L
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, NCTC13812_00781, NCTC6133_00899, ...Gene: BTN44_08795, CV021_09110, EP54_02745, EQ90_03735, ERS072840_01626, HMPREF3211_01094, NCTC10654_00855, NCTC11940_00723, NCTC13131_00828, NCTC13196_00435, NCTC13812_00781, NCTC6133_00899, NCTC7878_03402, NCTC9944_00829, SAMEA1469870_00860, 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: isolated from a natural source / Formula: C14H28O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.22 Å3/Da / Density % sol: 44.71 %
Crystal growTemperature: 293 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 temp room

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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: RAYONIX MX300-HS / Detector: CCD / Date: Feb 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.33→83.74 Å / Num. obs: 23124 / % possible obs: 98.2 % / Redundancy: 3.9 % / Biso Wilson estimate: 38 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.051 / Rrim(I) all: 0.1 / Net I/σ(I): 10.2
Reflection shellResolution: 2.33→2.41 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.813 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2250 / CC1/2: 0.748 / Rpim(I) all: 0.475 / Rrim(I) all: 0.942 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX(dev_3354: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MH9

6mh9


Resolution: 2.33→31.709 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 36.52 / Details: high disorder for residues B178-B185
RfactorNum. reflection% reflection
Rfree0.2883 1118 4.84 %
Rwork0.237 --
obs0.2396 23101 98.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.33→31.709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4456 0 32 134 4622
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024589
X-RAY DIFFRACTIONf_angle_d0.4776193
X-RAY DIFFRACTIONf_dihedral_angle_d3.5523319
X-RAY DIFFRACTIONf_chiral_restr0.043701
X-RAY DIFFRACTIONf_plane_restr0.002795
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3301-2.43610.36631200.31152743X-RAY DIFFRACTION98
2.4361-2.56450.35051360.30982763X-RAY DIFFRACTION97
2.5645-2.72510.36831310.29782715X-RAY DIFFRACTION98
2.7251-2.93530.34041280.27882756X-RAY DIFFRACTION98
2.9353-3.23050.35521690.26592721X-RAY DIFFRACTION98
3.2305-3.69730.25831080.22842806X-RAY DIFFRACTION98
3.6973-4.65580.25221570.20242749X-RAY DIFFRACTION99
4.6558-31.71210.26451690.21092730X-RAY DIFFRACTION98

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