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

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Basic information

Entry
Database: PDB / ID: 6cng
TitleThe X-ray crystal structure of the Streptococcus pneumoniae Fatty Acid Kinase (Fak) B3 protein loaded with linoleic acid to 1.47 Angstrom resolution
ComponentsFatty Acid Kinase (Fak) B3 protein
KeywordsTRANSFERASE / Streptococcus pneumoniae / Fatty acid kinase / Linoleic acid
Function / homology
Function and homology information


DegV, N-terminal domain, peripheral subdomain / Hypothetical Protein Tm841; Chain: A;domain 3 - #10 / Dihydroxyacetone kinase; domain 1 / DegV / DegV, C-terminal domain / Uncharacterised protein, DegV family COG1307 / DegV domain profile. / Hypothetical Protein Tm841; Chain: A;domain 3 / : / Rubrerythrin, domain 2 ...DegV, N-terminal domain, peripheral subdomain / Hypothetical Protein Tm841; Chain: A;domain 3 - #10 / Dihydroxyacetone kinase; domain 1 / DegV / DegV, C-terminal domain / Uncharacterised protein, DegV family COG1307 / DegV domain profile. / Hypothetical Protein Tm841; Chain: A;domain 3 / : / Rubrerythrin, domain 2 / Single Sheet / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / LINOLEIC ACID / DegV domain-containing protein spr0652
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsCuypers, M.G. / Subramanian, C. / White, S.W. / Rock, C.O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: The X-ray crystal structure of the Streptococcus pneumoniae Fatty Acid Kinase (Fak) B3 protein loaded with linoleic acid to 1.47 Angstrom resolution
Authors: Cuypers, M.G. / Subramanian, C. / White, S.W. / Rock, C.O.
History
DepositionMar 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fatty Acid Kinase (Fak) B3 protein
D: Fatty Acid Kinase (Fak) B3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,83224
Polymers65,7332
Non-polymers2,09922
Water14,322795
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A: Fatty Acid Kinase (Fak) B3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6569
Polymers32,8661
Non-polymers7908
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
D: Fatty Acid Kinase (Fak) B3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,17615
Polymers32,8661
Non-polymers1,30914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.775, 103.414, 67.469
Angle α, β, γ (deg.)90.00, 112.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein Fatty Acid Kinase (Fak) B3 protein


Mass: 32866.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (strain ATCC BAA-255 / R6) (bacteria)
Strain: ATCC BAA-255 / R6 / Gene: spr0652 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DQI6

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Non-polymers , 5 types, 817 molecules

#2: Chemical ChemComp-EIC / LINOLEIC ACID / 9,12-LINOLEIC ACID


Mass: 280.445 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H32O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 795 / 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: 2.58 Å3/Da / Density % sol: 52.4 % / Description: prismatic
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M Na acetate pH 4.6, 8% PEG 4000. Cryofreezing solution soak in motherliquor with 25% glycerol
Temp details: controlled temperature room

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Data collection

DiffractionMean temperature: 100 K
Ambient temp details: on cryostream (from Liq N2 flashfreeze)
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.47→62.11 Å / Num. obs: 108472 / % possible obs: 96.2 % / Redundancy: 3 % / Biso Wilson estimate: 17.283 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.025 / Rrim(I) all: 0.044 / Net I/σ(I): 15
Reflection shellResolution: 1.47→1.5 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.544 / Num. unique obs: 5188 / CC1/2: 0.574 / Rpim(I) all: 0.386 / Rrim(I) all: 0.669 / % possible all: 94.1

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3fdj (modified with MODBASE server)

3fdj


Resolution: 1.47→43.972 Å / Cross valid method: FREE R-VALUE / σ(F): 6.03 / Phase error: 19.34 / Details: H atoms are isotropic, not H atoms are anisotropic
RfactorNum. reflection% reflection
Rfree0.1647 5335 5.11 %
Rwork0.1365 --
obs0.1521 108436 96.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.47→43.972 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4298 0 140 795 5233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144496
X-RAY DIFFRACTIONf_angle_d1.1346048
X-RAY DIFFRACTIONf_dihedral_angle_d22.9871683
X-RAY DIFFRACTIONf_chiral_restr0.08702
X-RAY DIFFRACTIONf_plane_restr0.006778
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.49540.27972330.25814995X-RAY DIFFRACTION90
1.4954-1.52250.22482760.23695006X-RAY DIFFRACTION89
1.5225-1.55180.23032480.22855037X-RAY DIFFRACTION89
1.5518-1.58350.23522560.23195035X-RAY DIFFRACTION90
1.5835-1.61790.20652540.22025036X-RAY DIFFRACTION90
1.6179-1.65550.24172510.21525107X-RAY DIFFRACTION90
1.6555-1.69690.21722690.21055124X-RAY DIFFRACTION91
1.6969-1.74270.22272860.20445060X-RAY DIFFRACTION90
1.7427-1.79390.20342840.20315110X-RAY DIFFRACTION91
1.7939-1.85180.22462780.19885137X-RAY DIFFRACTION91
1.8518-1.91790.20912670.18635171X-RAY DIFFRACTION92
1.9179-1.99460.19172690.18015160X-RAY DIFFRACTION92
1.9946-2.08520.18792830.17475152X-RAY DIFFRACTION92
2.0852-2.1950.20242600.16335240X-RAY DIFFRACTION92
2.195-2.33220.18232590.15295238X-RAY DIFFRACTION93
2.3322-2.51180.18572520.14665258X-RAY DIFFRACTION93
2.5118-2.76370.16322630.13925244X-RAY DIFFRACTION93
2.7637-3.16170.1752730.12895272X-RAY DIFFRACTION93
3.1617-3.97590.15152880.11235321X-RAY DIFFRACTION93
3.9759-17.70430.15112870.10665337X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: 4.88 Å / Origin y: -6.4633 Å / Origin z: -0.3321 Å
111213212223313233
T0.0964 Å20.0035 Å2-0.0062 Å2-0.1312 Å20.007 Å2--0.131 Å2
L0.1819 °20.0072 °2-0.0185 °2-0.0964 °20.1618 °2--0.4733 °2
S-0.0084 Å °0.0003 Å °-0.0017 Å °0.001 Å °0.0057 Å °-0.0116 Å °0.0026 Å °-0.0046 Å °0.0051 Å °
Refinement TLS groupSelection details: all

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