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- PDB-5jki: Crystal structure of the first transmembrane PAP2 type phosphatid... -

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Basic information

Entry
Database: PDB / ID: 5jki
TitleCrystal structure of the first transmembrane PAP2 type phosphatidylglycerolphosphate phosphatase from Bacillus subtilis
ComponentsPutative lipid phosphate phosphatase YodM
KeywordsHYDROLASE / transmembrane PAP2 / phophatidylglycerol phosphate phosphatase
Function / homology
Function and homology information


phosphatidylglycerophosphatase / phosphatidylglycerophosphatase activity / plasma membrane
Similarity search - Function
Acid phosphatase homologues / Phosphatidic acid phosphatase type 2/haloperoxidase / PAP2 superfamily / Phosphatidic acid phosphatase type 2/haloperoxidase superfamily
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Unknown ligand / TUNGSTATE(VI)ION / Phosphatidylglycerophosphatase B
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsEl Ghachi, M. / Howe, N. / Lampion, A. / Delbrassine, F. / Vogeley, L. / Caffrey, M. / Sauvage, E. / Auger, R. / Guiseppe, A. / Roure, S. ...El Ghachi, M. / Howe, N. / Lampion, A. / Delbrassine, F. / Vogeley, L. / Caffrey, M. / Sauvage, E. / Auger, R. / Guiseppe, A. / Roure, S. / Perlier, S. / Mengin-lecreulx, D. / Foglino, M. / Touze, T.
Funding support Belgium, Ireland, 3items
OrganizationGrant numberCountry
Fonds de la Recherche Scientifique - FNRSMIS # F.4518.12 Belgium
BelspoIAP # P7/44 Belgium
Science Foundation Irelandgrant # 12/IA/1255 Ireland
CitationJournal: Cell. Mol. Life Sci. / Year: 2017
Title: Crystal structure and biochemical characterization of the transmembrane PAP2 type phosphatidylglycerol phosphate phosphatase from Bacillus subtilis.
Authors: Ghachi, M.E. / Howe, N. / Auger, R. / Lambion, A. / Guiseppi, A. / Delbrassine, F. / Manat, G. / Roure, S. / Peslier, S. / Sauvage, E. / Vogeley, L. / Rengifo-Gonzalez, J.C. / Charlier, P. / ...Authors: Ghachi, M.E. / Howe, N. / Auger, R. / Lambion, A. / Guiseppi, A. / Delbrassine, F. / Manat, G. / Roure, S. / Peslier, S. / Sauvage, E. / Vogeley, L. / Rengifo-Gonzalez, J.C. / Charlier, P. / Mengin-Lecreulx, D. / Foglino, M. / Touze, T. / Caffrey, M. / Kerff, F.
History
DepositionApr 26, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative lipid phosphate phosphatase YodM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7607
Polymers25,1561
Non-polymers6046
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint11 kcal/mol
Surface area11490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.066, 76.961, 99.629
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-432-

HOH

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Components

#1: Protein Putative lipid phosphate phosphatase YodM


Mass: 25155.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: yodM, BSU19650 / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43
References: UniProt: O34349, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Chemical ChemComp-WO4 / TUNGSTATE(VI)ION


Mass: 247.838 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: WO4
#3: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 4 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.67 Å3/Da / Density % sol: 53.92 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7
Details: 40 %(v/v) PEG-400, 0.1 M HEPES pH 7, 0.1 M lithium citrate tribasic tetra hydrate 0.1M sodium tungstate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.21458 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.21458 Å / Relative weight: 1
ReflectionResolution: 2.25→38.48 Å / Num. obs: 13107 / % possible obs: 100 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 11.3
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 12.9 % / Rmerge(I) obs: 1.02 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152)refinement
XDSdata reduction
XDSdata scaling
PHENIX(1.10_2152)phasing
RefinementMethod to determine structure: SAD / Resolution: 2.25→38.48 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.26
RfactorNum. reflection% reflection
Rfree0.2311 646 4.93 %
Rwork0.2008 --
obs0.2022 13107 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.25→38.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1595 0 62 39 1696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141698
X-RAY DIFFRACTIONf_angle_d0.8592276
X-RAY DIFFRACTIONf_dihedral_angle_d15.699613
X-RAY DIFFRACTIONf_chiral_restr0.084260
X-RAY DIFFRACTIONf_plane_restr0.005270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2501-2.42380.23951320.20332438X-RAY DIFFRACTION100
2.4238-2.66760.24611470.18032440X-RAY DIFFRACTION100
2.6676-3.05350.21181310.16972459X-RAY DIFFRACTION100
3.0535-3.84650.2104950.18962540X-RAY DIFFRACTION100
3.8465-38.48610.24021410.22212584X-RAY DIFFRACTION100

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