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- PDB-5jwy: Structure of lipid phosphate phosphatase PgpB complex with PE -

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Basic information

Entry
Database: PDB / ID: 5jwy
TitleStructure of lipid phosphate phosphatase PgpB complex with PE
ComponentsPhosphatidylglycerophosphatase B
KeywordsHYDROLASE / transmembrane helices / protein-lipid complex / enzyme
Function / homology
Function and homology information


diacylglycerol diphosphate phosphatase / diacylglycerol diphosphate phosphatase activity / phosphatidate phosphatase / phosphatidylglycerophosphatase / undecaprenyl-diphosphate phosphatase / phosphatidylglycerol biosynthetic process / phosphatidate phosphatase activity / undecaprenyl-diphosphatase activity / phosphatidylglycerophosphatase activity / glycerophospholipid biosynthetic process ...diacylglycerol diphosphate phosphatase / diacylglycerol diphosphate phosphatase activity / phosphatidate phosphatase / phosphatidylglycerophosphatase / undecaprenyl-diphosphate phosphatase / phosphatidylglycerol biosynthetic process / phosphatidate phosphatase activity / undecaprenyl-diphosphatase activity / phosphatidylglycerophosphatase activity / glycerophospholipid biosynthetic process / phospholipid catabolic process / peptidoglycan biosynthetic process / cell outer membrane / plasma membrane
Similarity search - Function
Acid phosphatase homologues / Phosphatidic acid phosphatase type 2/haloperoxidase / Vanadium-containing Chloroperoxidase; domain 1 / Phosphatidic acid phosphatase type 2/haloperoxidase / PAP2 superfamily / Phosphatidic acid phosphatase type 2/haloperoxidase superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-46E / Phosphatidylglycerophosphatase B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsTong, S. / Wang, M. / Zheng, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM097290 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Insight into Substrate Selection and Catalysis of Lipid Phosphate Phosphatase PgpB in the Cell Membrane.
Authors: Tong, S. / Lin, Y. / Lu, S. / Wang, M. / Bogdanov, M. / Zheng, L.
History
DepositionMay 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Sep 7, 2016Group: Database references
Revision 1.3Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.5Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Phosphatidylglycerophosphatase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5822
Polymers29,9461
Non-polymers6361
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.533, 73.593, 132.095
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phosphatidylglycerophosphatase B / Diacylglycerol pyrophosphate phosphatase / DGPP phosphatase / Phosphatidate phosphatase / ...Diacylglycerol pyrophosphate phosphatase / DGPP phosphatase / Phosphatidate phosphatase / Undecaprenyl pyrophosphate phosphatase / Undecaprenyl-diphosphatase


Mass: 29946.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: pgpB, b1278, JW1270 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3)
References: UniProt: P0A924, phosphatidylglycerophosphatase, EC: 3.1.3.81, phosphatidate phosphatase, undecaprenyl-diphosphate phosphatase
#2: Chemical ChemComp-46E / (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl tetradecanoate


Mass: 635.853 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H66NO8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.21 Å3/Da / Density % sol: 61.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG6000, sodium chloride, ADA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 20, 2010
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionRedundancy: 14 % / Number: 95967 / Rsym value: 0.102 / D res high: 3.2 Å / D res low: 132.095 Å / Num. obs: 6838 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRsym valueRedundancy
10.1273.5910.0190.01911.2
7.1610.1210.0280.02813
5.847.1610.0630.06313.7
5.065.8410.0780.07813.9
4.535.0610.0710.07114.1
4.134.5310.0950.09514.3
3.824.1310.1630.16314.1
3.583.8210.3070.30714.4
3.373.5810.5010.50114.4
3.23.3710.7780.77814.5
ReflectionResolution: 3.2→132.1 Å / Num. obs: 6838 / % possible obs: 100 % / Redundancy: 14 % / Rsym value: 0.102 / Net I/av σ(I): 7.048 / Net I/σ(I): 25.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.2-3.3714.50.77811100
3.37-3.5814.40.5011.41100
3.58-3.8214.40.3072.21100
3.82-4.1314.10.1634.71100
4.13-4.5314.30.09581100
4.53-5.0614.10.07110.21100
5.06-5.8413.90.0789.61100
5.84-7.1613.70.063121100
7.16-10.12130.02822.11100
10.12-73.59311.20.01931.4198.9

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Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.2→132.1 Å / Cor.coef. Fo:Fc: 0.877 / Cor.coef. Fo:Fc free: 0.879 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.572 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3051 323 4.8 %RANDOM
Rwork0.2672 ---
obs0.2691 6800 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 173.15 Å2 / Biso mean: 93.591 Å2 / Biso min: 49.44 Å2
Baniso -1Baniso -2Baniso -3
1-2.21 Å20 Å2-0 Å2
2--10.62 Å2-0 Å2
3----12.84 Å2
Refinement stepCycle: final / Resolution: 3.2→132.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2104 0 43 2 2149
Biso mean--95.23 52.19 -
Num. residues----259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192214
X-RAY DIFFRACTIONr_bond_other_d00.022195
X-RAY DIFFRACTIONr_angle_refined_deg1.2761.9423013
X-RAY DIFFRACTIONr_angle_other_deg3.4683.0115016
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5455258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.18121.66790
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.08715339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8421518
X-RAY DIFFRACTIONr_chiral_restr0.0610.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212394
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02546
X-RAY DIFFRACTIONr_mcbond_it4.4389.0351035
X-RAY DIFFRACTIONr_mcbond_other4.4399.0341034
X-RAY DIFFRACTIONr_mcangle_it7.2113.5321292
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 22 -
Rwork0.328 475 -
all-497 -
obs--100 %

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