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

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Basic information

Entry
Database: PDB / ID: 5woo
TitleThe crystal structure of the Staphylococcus aureus Fatty acid Kinase (Fak) B1 protein loaded with Myristic acid (C14:0) to 1.78 Angstrom resolution
ComponentsEDD domain protein, DegV family
KeywordsTRANSFERASE / Staphylococcus aureus / FakB1 / myristic acid / C14:0
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
MYRISTIC ACID / DegV domain-containing protein / DegV domain-containing protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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 2, 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

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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)66,0235
Polymers65,4742
Non-polymers5493
Water11,746652
1
A: EDD domain protein, DegV family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0583
Polymers32,7371
Non-polymers3202
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)32,9662
Polymers32,7371
Non-polymers2281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.393, 54.453, 84.907
Angle α, β, γ (deg.)104.89, 90.20, 107.76
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


Mass: 32737.215 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-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 652 / 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: 2.18 Å3/Da / Density % sol: 43.65 %
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: temperature controlled room

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: N2liq. flash frozen crystal
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→81.73 Å / Num. obs: 50586 / % possible obs: 96.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 19.68 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.051 / Rrim(I) all: 0.1 / Net I/σ(I): 9.8
Reflection shellResolution: 1.78→1.82 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.576 / Mean I/σ(I) obs: 2 / Num. unique obs: 2913 / CC1/2: 0.736 / Rpim(I) all: 0.395 / Rrim(I) all: 0.783 / % possible all: 95.9

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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: 1.78→36.9 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 20.03
RfactorNum. reflection% reflection
Rfree0.2002 2306 4.56 %
Rwork0.1509 --
obs0.1531 50576 96.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.78→36.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4495 0 38 652 5185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064755
X-RAY DIFFRACTIONf_angle_d0.8016428
X-RAY DIFFRACTIONf_dihedral_angle_d12.5982898
X-RAY DIFFRACTIONf_chiral_restr0.055719
X-RAY DIFFRACTIONf_plane_restr0.005831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.81870.28051690.2293032X-RAY DIFFRACTION96
1.8187-1.8610.29451490.21422962X-RAY DIFFRACTION94
1.861-1.90760.23111640.1892968X-RAY DIFFRACTION97
1.9076-1.95910.22231520.1833056X-RAY DIFFRACTION95
1.9591-2.01680.22861230.17623015X-RAY DIFFRACTION97
2.0168-2.08190.24751450.16733031X-RAY DIFFRACTION96
2.0819-2.15630.21781490.16282984X-RAY DIFFRACTION97
2.1563-2.24260.2181510.15833068X-RAY DIFFRACTION96
2.2426-2.34460.18661550.14623038X-RAY DIFFRACTION97
2.3446-2.46820.19931410.15163030X-RAY DIFFRACTION97
2.4682-2.62280.21361440.15223039X-RAY DIFFRACTION97
2.6228-2.82530.21231480.14713035X-RAY DIFFRACTION97
2.8253-3.10950.19521270.14563058X-RAY DIFFRACTION97
3.1095-3.55910.1661400.13273017X-RAY DIFFRACTION96
3.5591-4.48280.16931350.12042968X-RAY DIFFRACTION94
4.4828-36.90780.18441140.15332969X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 0.1568 Å / Origin y: 0.5957 Å / Origin z: -0.3204 Å
111213212223313233
T0.1304 Å20.0037 Å20.0145 Å2-0.1691 Å20.0077 Å2--0.1723 Å2
L0.0866 °20.0555 °20.0743 °2-0.3466 °20.5024 °2--0.9844 °2
S-0.0101 Å °0.0065 Å °-0.0121 Å °-0.0099 Å °-0.0404 Å °0.0088 Å °-0.0297 Å °0.0236 Å °0.0539 Å °
Refinement TLS groupSelection details: all

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