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- PDB-1u7n: Crystal Structure of the fatty acid/phospholipid synthesis protei... -

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Basic information

Entry
Database: PDB / ID: 1u7n
TitleCrystal Structure of the fatty acid/phospholipid synthesis protein PlsX from Enterococcus faecalis V583
ComponentsFatty acid/phospholipid synthesis protein plsX
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / fatty acid/phospholipid synthesis / PlsX / Enterococcus faecalis V583 / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


phosphate acyltransferase / phosphate:acyl-[acyl carrier protein] acyltransferase activity / phospholipid biosynthetic process / fatty acid biosynthetic process / cytoplasm
Similarity search - Function
Fatty acid synthesis PlsX protein / Phospholipid biosynthesis protein, PlsX-like / Fatty acid synthesis protein / Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ETHANOL / Phosphate acyltransferase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.26 Å
AuthorsKim, Y. / Li, H. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.STRUCT.FUNCT.GENOM. / Year: 2009
Title: Crystal structure of fatty acid/phospholipid synthesis protein PlsX from Enterococcus faecalis.
Authors: Kim, Y. / Li, H. / Binkowski, T.A. / Holzle, D. / Joachimiak, A.
History
DepositionAug 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fatty acid/phospholipid synthesis protein plsX
B: Fatty acid/phospholipid synthesis protein plsX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7667
Polymers73,5202
Non-polymers2465
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-18 kcal/mol
Surface area26070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.362, 82.423, 147.237
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/phospholipid synthesis protein plsX


Mass: 36760.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: plsX / Plasmid details: T7 promoter / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q82ZE8
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.56 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Ethanol, HEPES, MgCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: SBC-2 / Detector: CCD / Date: Jul 22, 2004 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.26→73.52 Å / Num. all: 38309 / Num. obs: 36201 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 5.4
Reflection shellResolution: 2.26→2.34 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3373 / % possible all: 94.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0000refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.26→73.52 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.898 / SU B: 6.398 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.301 / ESU R Free: 0.237
RfactorNum. reflection% reflectionSelection details
Rfree0.26178 1804 5 %RANDOM
Rwork0.20615 ---
all0.2089 34335 --
obs0.2089 34335 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.698 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å20 Å2
2--0.53 Å20 Å2
3----1.1 Å2
Refinement stepCycle: LAST / Resolution: 2.26→73.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4972 0 4 319 5295
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225067
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.9776854
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3495668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.94425.981214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.87115925
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1341519
X-RAY DIFFRACTIONr_chiral_restr0.110.2788
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023787
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.22633
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2314
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.229
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.9061.53367
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.20525234
X-RAY DIFFRACTIONr_scbond_it2.11231884
X-RAY DIFFRACTIONr_scangle_it3.224.51620
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.262→2.321 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.298 122
Rwork0.241 2426
obs-2426

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