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- PDB-6dj6: The X-ray crystal structure of the Streptococcus pneumoniae Fatty... -

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Basic information

Entry
Database: PDB / ID: 6dj6
TitleThe X-ray crystal structure of the Streptococcus pneumoniae Fatty Acid Kinase (Fak) B2 protein loaded with cis-oleic acid to 1.9 Angstrom resolution
ComponentsFatty Acid Kinase (Fak) B2 protein (SPR1019)
KeywordsTRANSFERASE / Streptococcus pneumoniae / Fatty acid kinase / oleic acid
Function / homology
Function and homology information


Hypothetical Protein Tm841; Chain: A;domain 3 - #10 / Rossmann fold - #10170 / DegV / DegV, C-terminal domain / Uncharacterised protein, DegV family COG1307 / DegV domain profile. / Hypothetical Protein Tm841; Chain: A;domain 3 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
OLEIC ACID / DegV family EDD domain-containing protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 the Streptococcus pneumoniae Fatty Acid Kinase (Fak) B2 protein (SPR1019) loaded with cis-oleic acid to 1.9 Angstrom resolution
Authors: Cuypers, M.G. / Subramanian, C. / White, S.W. / Rock, C.O.
History
DepositionMay 24, 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: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: 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) B2 protein (SPR1019)
B: Fatty Acid Kinase (Fak) B2 protein (SPR1019)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,69710
Polymers68,6482
Non-polymers1,0488
Water9,926551
1
A: Fatty Acid Kinase (Fak) B2 protein (SPR1019)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9987
Polymers34,3241
Non-polymers6746
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fatty Acid Kinase (Fak) B2 protein (SPR1019)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6993
Polymers34,3241
Non-polymers3752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.720, 103.851, 108.174
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fatty Acid Kinase (Fak) B2 protein (SPR1019)


Mass: 34324.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: SPR1019 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0I9AIE4
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 551 / 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: 2.45 Å3/Da / Density % sol: 49.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1M HEPES pH 7.4, 10% v/v isopropanol, 20% w/v PEG4000
Temp details: controlled temperature room

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: pre frozen in Liquid N2
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: 1.9→74.92 Å / Num. obs: 52631 / % possible obs: 98.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 17.034 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.067 / Rrim(I) all: 0.129 / Χ2: 0.95 / Net I/σ(I): 9.4
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3366 / CC1/2: 0.479 / Rpim(I) all: 0.51 / Rrim(I) all: 0.896 / Χ2: 1.07 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MODBASE sequence based generated 3D model

Resolution: 1.9→54.15 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.349 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.14 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22655 2659 5.1 %RANDOM
Rwork0.17053 ---
obs0.17333 49927 97.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.118 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å2-0 Å2
2--1.86 Å2-0 Å2
3----1.98 Å2
Refinement stepCycle: 1 / Resolution: 1.9→54.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4282 0 71 551 4904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0144540
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174370
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.6576132
X-RAY DIFFRACTIONr_angle_other_deg0.9231.6710247
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3355582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.40224.762189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.26615864
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5511514
X-RAY DIFFRACTIONr_chiral_restr0.0650.2618
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024996
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02752
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6792.1592292
X-RAY DIFFRACTIONr_mcbond_other1.6792.1592291
X-RAY DIFFRACTIONr_mcangle_it2.5453.2322886
X-RAY DIFFRACTIONr_mcangle_other2.5453.2322887
X-RAY DIFFRACTIONr_scbond_it2.9632.5352248
X-RAY DIFFRACTIONr_scbond_other2.9622.5352249
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7183.6413247
X-RAY DIFFRACTIONr_long_range_B_refined6.33527.3095156
X-RAY DIFFRACTIONr_long_range_B_other6.33427.3085157
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 202 -
Rwork0.27 3648 -
obs--99.48 %

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