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- PDB-6dke: The X-ray crystal structure of Streptococcus pneumoniae Fatty Aci... -

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Basic information

Entry
Database: PDB / ID: 6dke
TitleThe X-ray crystal structure of Streptococcus pneumoniae Fatty Acid Kinase (Fak) B1 protein loaded with palmitic acid (C16:0) to 1.76 Angstrom resolution
ComponentsFatty Acid Kinase (Fak) B1 protein
KeywordsTRANSFERASE / Streptococcus pneumoniae / Fatty acid kinase / oleic acid
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 spr1415
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsCuypers, M.G. / Subramanian, C. / White, S.W. / Rock, C.O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: To Be Published
Title: The X-ray crystal structure of Streptococcus pneumoniae Fatty Acid Kinase (Fak) B1 protein loaded with palmitic acid (C16:0) to 1.76 Angstrom resolution
Authors: Cuypers, M.G. / Subramanian, C. / White, S.W. / Rock, C.O.
History
DepositionMay 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Fatty Acid Kinase (Fak) B1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7942
Polymers34,5381
Non-polymers2561
Water4,954275
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.825, 62.337, 50.430
Angle α, β, γ (deg.)90.00, 95.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fatty Acid Kinase (Fak) B1 protein


Mass: 34538.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DP17
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.12 Å3/Da / Density % sol: 42.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M MES pH6.5, 30% (w/v) PEG4000 / Temp details: controlled temperature room

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→62.34 Å / Num. obs: 28063 / % possible obs: 97.9 % / Redundancy: 2.7 % / Biso Wilson estimate: 22 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.042 / Rrim(I) all: 0.072 / Χ2: 0.88 / Net I/σ(I): 10.6
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2 / Num. unique obs: 1592 / CC1/2: 0.746 / Rpim(I) all: 0.355 / Rrim(I) all: 0.613 / Χ2: 0.89 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→46.574 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.29
RfactorNum. reflection% reflection
Rfree0.2062 2614 5.01 %
Rwork0.1696 --
obs0.1714 52190 92.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.76→46.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2185 0 18 275 2478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052274
X-RAY DIFFRACTIONf_angle_d0.7513079
X-RAY DIFFRACTIONf_dihedral_angle_d21.13844
X-RAY DIFFRACTIONf_chiral_restr0.055355
X-RAY DIFFRACTIONf_plane_restr0.004396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.7920.3421600.30462627X-RAY DIFFRACTION93
1.792-1.82650.28221290.27172636X-RAY DIFFRACTION94
1.8265-1.86380.28331610.24022615X-RAY DIFFRACTION93
1.8638-1.90430.2351090.22282632X-RAY DIFFRACTION93
1.9043-1.94860.25721340.21052677X-RAY DIFFRACTION93
1.9486-1.99730.24161260.19722547X-RAY DIFFRACTION92
1.9973-2.05130.24031750.18852545X-RAY DIFFRACTION91
2.0513-2.11170.25891380.18292485X-RAY DIFFRACTION89
2.1117-2.17990.19111460.17362668X-RAY DIFFRACTION96
2.1799-2.25780.23131670.16632684X-RAY DIFFRACTION96
2.2578-2.34820.23421470.16232648X-RAY DIFFRACTION95
2.3482-2.4550.19361390.16492663X-RAY DIFFRACTION95
2.455-2.58440.20321580.15842667X-RAY DIFFRACTION94
2.5844-2.74640.18821230.17132594X-RAY DIFFRACTION92
2.7464-2.95840.20271140.15922492X-RAY DIFFRACTION88
2.9584-3.2560.19751460.16262603X-RAY DIFFRACTION94
3.256-3.7270.18791270.14362658X-RAY DIFFRACTION94
3.727-4.69490.16691080.13812592X-RAY DIFFRACTION91
4.6949-46.59030.18871070.18152543X-RAY DIFFRACTION89

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