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

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Basic information

Entry
Database: PDB / ID: 6alw
TitleThe crystal structure of the Staphylococcus aureus Fatty acid Kinase (Fak) B1 protein loaded with 12-Methyl Myristic Acid (C15:0) to 1.63 Angstrom resolution
ComponentsEDD domain protein, DegV family
KeywordsTRANSFERASE / Staphylococcus aureus / FakB1 / 12-Methyl Myristic Acid / 12-Methyltetradecanoic acid / C15:0
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
(12R)-12-methyltetradecanoic acid / (12S)-12-methyltetradecanoic acid / DegV domain-containing protein / DegV domain-containing protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsCuypers, M.G. / Ericson, M. / Subramanian, C. / White, S.W. / Rock, C.O.
Funding support United States, 1items
OrganizationGrant numberCountry
St. Jude Children's Research Hospital (ALSAC) United States
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
DepositionAug 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 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 1.2Jan 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 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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

Downloads & links

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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)65,90914
Polymers64,2032
Non-polymers1,70612
Water15,097838
1
A: EDD domain protein, DegV family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1399
Polymers32,1021
Non-polymers1,0378
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)32,7705
Polymers32,1021
Non-polymers6694
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.348, 54.529, 84.415
Angle α, β, γ (deg.)105.13, 90.00, 107.81
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 / Fatty acid-binding protein DegV / FakB1 protein


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, UniProt: P0A0N2*PLUS
#2: Chemical ChemComp-BNV / (12S)-12-methyltetradecanoic acid


Mass: 242.397 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H30O2
#3: Chemical ChemComp-BMJ / (12R)-12-methyltetradecanoic acid


Mass: 242.397 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H30O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 838 / 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: 2.19 Å3/Da / Density % sol: 43.81 %
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 room temperature

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: crystal flash frozen in Liq. N2
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.63→81.18 Å / Num. obs: 66112 / % possible obs: 97.2 % / Redundancy: 4 % / Biso Wilson estimate: 7.76 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.106 / Rrim(I) all: 0.212 / Net I/σ(I): 8.6
Reflection shellResolution: 1.63→1.66 Å / Redundancy: 4 % / Rmerge(I) obs: 0.906 / Mean I/σ(I) obs: 2 / Num. unique obs: 3294 / CC1/2: 0.662 / Rpim(I) all: 0.524 / % possible all: 95.2

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UTO

5uto


Resolution: 1.63→40.591 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 19.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1967 3305 5 %random
Rwork0.1549 ---
obs0.1571 66100 97.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.63→40.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4453 0 116 838 5407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014856
X-RAY DIFFRACTIONf_angle_d0.9526561
X-RAY DIFFRACTIONf_dihedral_angle_d13.6342960
X-RAY DIFFRACTIONf_chiral_restr0.067727
X-RAY DIFFRACTIONf_plane_restr0.006849
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.65330.27431400.2512613X-RAY DIFFRACTION95
1.6533-1.6780.27831340.23452556X-RAY DIFFRACTION96
1.678-1.70420.2371330.22792575X-RAY DIFFRACTION96
1.7042-1.73210.26611220.21192563X-RAY DIFFRACTION96
1.7321-1.7620.261520.20942615X-RAY DIFFRACTION96
1.762-1.7940.24631160.19382589X-RAY DIFFRACTION96
1.794-1.82850.23211070.182594X-RAY DIFFRACTION96
1.8285-1.86590.21591440.17232615X-RAY DIFFRACTION96
1.8659-1.90640.17541400.16812569X-RAY DIFFRACTION97
1.9064-1.95080.22791310.17442637X-RAY DIFFRACTION96
1.9508-1.99960.2341120.17252596X-RAY DIFFRACTION97
1.9996-2.05360.24321510.16892568X-RAY DIFFRACTION97
2.0536-2.11410.16371700.14972634X-RAY DIFFRACTION97
2.1141-2.18230.19981550.14922620X-RAY DIFFRACTION97
2.1823-2.26030.2141240.14832613X-RAY DIFFRACTION97
2.2603-2.35080.18021480.14912591X-RAY DIFFRACTION98
2.3508-2.45770.21331570.15122599X-RAY DIFFRACTION98
2.4577-2.58730.19221370.15612720X-RAY DIFFRACTION98
2.5873-2.74940.17481110.14672638X-RAY DIFFRACTION98
2.7494-2.96160.20531300.14432612X-RAY DIFFRACTION98
2.9616-3.25950.18971460.13892691X-RAY DIFFRACTION99
3.2595-3.73090.17411630.12082644X-RAY DIFFRACTION99
3.7309-4.69940.14361400.10922662X-RAY DIFFRACTION99
4.6994-40.60330.1621420.14082681X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 0.2649 Å / Origin y: -0.9655 Å / Origin z: -0.289 Å
111213212223313233
T0.0331 Å2-0.004 Å2-0.0006 Å2-0.0479 Å20.0023 Å2--0.0556 Å2
L0.0831 °2-0.0291 °2-0.0454 °2-0.2573 °20.3004 °2--0.78 °2
S-0.0142 Å °-0.006 Å °0.0033 Å °0.0118 Å °-0.0101 Å °0.0109 Å °0.0067 Å °0.0172 Å °0.0118 Å °
Refinement TLS groupSelection details: all

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