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- PDB-6nr1: The X-ray crystal structure of Streptococcus pneumoniae Fatty Aci... -

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Basic information

Entry
Database: PDB / ID: 6nr1
TitleThe X-ray crystal structure of Streptococcus pneumoniae Fatty Acid Kinase (Fak) B2 protein loaded with Vaccenic acid (C18:1 delta11) to 2.1 Angstrom resolution
ComponentsFatty Acid Kinase (Fak) B2 protein (SPR1019)
KeywordsTRANSFERASE / Streptococcus pneumoniae / Fatty acid kinase / Vaccenic 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 ...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
VACCENIC ACID / DegV family EDD domain-containing protein / DegV domain-containing protein spr1019
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCuypers, M.G. / Gullett, J.M. / 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) B2 protein loaded with Vaccenic acid (C18:1 delta11) to 2.1 Angstrom resolution
Authors: Cuypers, M.G. / Gullett, J.M. / Subramanian, C. / White, S.W. / Rock, C.O.
History
DepositionJan 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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: Fatty Acid Kinase (Fak) B2 protein (SPR1019)
B: Fatty Acid Kinase (Fak) B2 protein (SPR1019)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4907
Polymers68,6482
Non-polymers8415
Water9,026501
1
A: Fatty Acid Kinase (Fak) B2 protein (SPR1019)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8835
Polymers34,3241
Non-polymers5594
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)34,6072
Polymers34,3241
Non-polymers2821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.655, 103.409, 107.925
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, UniProt: Q8DPT4*PLUS
#2: Chemical ChemComp-VCA / VACCENIC ACID / (11E)-OCTADEC-11-ENOIC ACID


Mass: 282.461 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C18H34O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 501 / 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: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growTemperature: 290 K / Method: vapor diffusion
Details: 18% w/v PEG3350, 4.8% v/v 2-Propanol, 0.1M CAPSO pH 9.0, 17% v/v PEG400 (LMB D12)
Temp details: controlled temp. room

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Data collection

DiffractionMean temperature: 100 K
Ambient temp details: flash frozen in liq N2 then cryostream
Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→74.67 Å / Num. obs: 39625 / % possible obs: 99.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 21.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.05 / Rrim(I) all: 0.113 / Χ2: 0.63 / Net I/σ(I): 9
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 2 / Num. unique obs: 3194 / CC1/2: 0.799 / Rpim(I) all: 0.311 / Rrim(I) all: 0.693 / Χ2: 0.61 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(dev_3354: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DJ6

6dj6


Resolution: 2.1→52.21 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.58
RfactorNum. reflection% reflection
Rfree0.2412 1946 4.92 %
Rwork0.1843 --
obs0.1871 39546 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→52.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4291 0 58 501 4850
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094522
X-RAY DIFFRACTIONf_angle_d0.9156110
X-RAY DIFFRACTIONf_dihedral_angle_d13.1182785
X-RAY DIFFRACTIONf_chiral_restr0.057722
X-RAY DIFFRACTIONf_plane_restr0.005775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.15250.26731530.20692627X-RAY DIFFRACTION100
2.1525-2.21070.2791420.20412661X-RAY DIFFRACTION99
2.2107-2.27580.28091260.20482610X-RAY DIFFRACTION99
2.2758-2.34920.26671440.19932638X-RAY DIFFRACTION99
2.3492-2.43320.27361370.19652654X-RAY DIFFRACTION100
2.4332-2.53060.28921500.1962651X-RAY DIFFRACTION100
2.5306-2.64580.2481230.18492703X-RAY DIFFRACTION100
2.6458-2.78530.24331440.18172654X-RAY DIFFRACTION100
2.7853-2.95980.22881440.16572676X-RAY DIFFRACTION100
2.9598-3.18820.22881340.16582710X-RAY DIFFRACTION100
3.1882-3.5090.21291250.1642727X-RAY DIFFRACTION100
3.509-4.01660.2141940.16252768X-RAY DIFFRACTION100
4.0166-5.05990.21221360.15632735X-RAY DIFFRACTION99
5.0599-52.22610.25151940.24612786X-RAY DIFFRACTION98

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