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- PDB-6mh9: The crystal structure of the Staphylococcus aureus Fatty acid Kin... -

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Basic information

Entry
Database: PDB / ID: 6mh9
TitleThe crystal structure of the Staphylococcus aureus Fatty acid Kinase (Fak) B1 protein A121I mutant to 2.02 Angstrom resolution
ComponentsFatty Acid Kinase (Fak) B1 protein
KeywordsTRANSFERASE / Staphylococcus aureus / FakB1 / mutant TRANSFERASE
Function / homology
Function and homology information


: / 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: 2.02 Å
AuthorsCuypers, M.G. / Ericson, M. / Subramanian, C. / White, S.W. / Rock, C.O.
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
DepositionSep 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: 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

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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)65,0764
Polymers64,5632
Non-polymers5132
Water3,729207
1
A: Fatty Acid Kinase (Fak) B1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5382
Polymers32,2821
Non-polymers2561
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)32,5382
Polymers32,2821
Non-polymers2561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.505, 53.892, 86.039
Angle α, β, γ (deg.)103.74, 90.39, 107.26
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: 32281.729 Da / Num. of mol.: 2 / Mutation: A121I
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
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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.11 Å3/Da / Density % sol: 41.68 %
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: stable room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.6039 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: 1.6039 Å / Relative weight: 1
ReflectionResolution: 2.02→83.29 Å / Num. obs: 34458 / % possible obs: 94.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 34.8 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.039 / Rrim(I) all: 0.077 / Net I/σ(I): 12.3
Reflection shellResolution: 2.02→2.07 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.585 / Num. unique obs: 2509 / CC1/2: 0.724 / Rpim(I) all: 0.438 / Rrim(I) all: 0.849 / % possible all: 91.3

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
SCALAaimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UTO

5uto


Resolution: 2.02→48.441 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 30.09
RfactorNum. reflection% reflection
Rfree0.2588 1665 4.83 %
Rwork0.2069 --
obs0.2095 34453 94.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.02→48.441 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4461 0 36 207 4704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024660
X-RAY DIFFRACTIONf_angle_d0.4496293
X-RAY DIFFRACTIONf_dihedral_angle_d5.0173898
X-RAY DIFFRACTIONf_chiral_restr0.042704
X-RAY DIFFRACTIONf_plane_restr0.003808
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.07950.33981270.28732675X-RAY DIFFRACTION91
2.0795-2.14660.33871670.26492643X-RAY DIFFRACTION93
2.1466-2.22330.32181100.2512666X-RAY DIFFRACTION91
2.2233-2.31230.321340.23242717X-RAY DIFFRACTION95
2.3123-2.41760.28761410.22332695X-RAY DIFFRACTION92
2.4176-2.5450.28151340.22722758X-RAY DIFFRACTION95
2.545-2.70440.30221370.2222755X-RAY DIFFRACTION95
2.7044-2.91320.23641070.21572760X-RAY DIFFRACTION95
2.9132-3.20640.2681460.21422791X-RAY DIFFRACTION96
3.2064-3.67020.24591570.22749X-RAY DIFFRACTION96
3.6702-4.62350.22691520.17852775X-RAY DIFFRACTION97
4.6235-48.45530.23561530.18952804X-RAY DIFFRACTION97

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