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

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Basic information

Entry
Database: PDB / ID: 6nok
TitleThe X-ray crystal structure of Streptococcus pneumoniae Fatty Acid Kinase (Fak) B1 protein loaded with myristic acid (C14:0) to 1.69 Angstrom resolution
ComponentsFatty Acid Kinase (Fak) B1 protein
KeywordsTRANSFERASE / Streptococcus pneumoniae / Fatty acid kinase / myristic 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
MYRISTIC ACID / DegV domain-containing protein spr1415
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 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) B1 protein loaded with myristic acid (C14:0) to 1.69 Angstrom resolution
Authors: Cuypers, M.G. / Gullett, J.M. / Subramanian, C. / White, S.W. / Rock, C.O.
History
DepositionJan 16, 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

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Assembly

Deposited unit
A: Fatty Acid Kinase (Fak) B1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7893
Polymers34,5381
Non-polymers2512
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.556, 66.324, 46.953
Angle α, β, γ (deg.)90.00, 95.75, 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-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 287 / 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: 1.69 Å3/Da / Density % sol: 27.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES PH6.5, 30% (W/V) PEG4000 (Qiagen PEG2 / D7)
Temp details: controlled temperature room

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Dec 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→66.32 Å / Num. obs: 25680 / % possible obs: 99.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 17.3 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.034 / Rrim(I) all: 0.066 / Χ2: 1.05 / Net I/av σ(I): 10.9 / Net I/σ(I): 16.2
Reflection shellResolution: 1.69→1.72 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 2 / Num. unique obs: 1310 / CC1/2: 0.667 / Rpim(I) all: 0.415 / Rrim(I) all: 0.79 / Χ2: 1.03 / % possible all: 99.8

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Processing

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

6dke


Resolution: 1.69→38.193 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.25
RfactorNum. reflection% reflection
Rfree0.1998 1209 4.71 %
Rwork0.1523 --
obs0.1545 25659 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.69→38.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2189 0 17 287 2493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172348
X-RAY DIFFRACTIONf_angle_d1.4823190
X-RAY DIFFRACTIONf_dihedral_angle_d9.7571901
X-RAY DIFFRACTIONf_chiral_restr0.1359
X-RAY DIFFRACTIONf_plane_restr0.01421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.75770.28451360.22172706X-RAY DIFFRACTION100
1.7577-1.83770.3021460.20172673X-RAY DIFFRACTION100
1.8377-1.93460.22321180.16622728X-RAY DIFFRACTION100
1.9346-2.05580.17881210.15262720X-RAY DIFFRACTION100
2.0558-2.21450.21631510.14542725X-RAY DIFFRACTION100
2.2145-2.43730.21381290.1522693X-RAY DIFFRACTION100
2.4373-2.78990.18631450.15212714X-RAY DIFFRACTION100
2.7899-3.51460.17541300.14212734X-RAY DIFFRACTION100
3.5146-38.2030.18231330.14222757X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 8.1024 Å / Origin y: -0.5188 Å / Origin z: 9.0119 Å
111213212223313233
T0.131 Å2-0.001 Å2-0.0273 Å2-0.1167 Å20.0037 Å2--0.1253 Å2
L0.7698 °20.1579 °2-0.2639 °2-0.9183 °2-0.1101 °2--1.0911 °2
S0.0158 Å °-0.0309 Å °0.017 Å °0.0489 Å °-0.0232 Å °0.0346 Å °-0.0384 Å °-0.0318 Å °0.0021 Å °
Refinement TLS groupSelection details: all

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