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- PDB-6fmx: IMISX-EP of W-PgpB -

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Basic information

Entry
Database: PDB / ID: 6fmx
TitleIMISX-EP of W-PgpB
ComponentsPhosphatidylglycerophosphatase B
KeywordsHYDROLASE / Serial crystallography / experimental phasing / in meso crystallization / in situ diffraction data collection / membrane protein structure. / MEMBRANE PROTEIN
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 / TUNGSTATE(VI)ION / Phosphatidylglycerophosphatase B
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.79 Å
AuthorsHuang, C.-Y. / Olieric, V. / Howe, N. / Warshamanage, R. / Weinert, T. / Panepucci, E. / Vogeley, L. / Basu, S. / Diederichs, K. / Caffrey, M. / Wang, M.
Funding support Ireland, Switzerland, 2items
OrganizationGrant numberCountry
Science Foundation Ireland16/IA/4435 Ireland
European Union701647 Switzerland
CitationJournal: Commun Biol / Year: 2018
Title: In situ serial crystallography for rapid de novo membrane protein structure determination.
Authors: Huang, C.Y. / Olieric, V. / Howe, N. / Warshamanage, R. / Weinert, T. / Panepucci, E. / Vogeley, L. / Basu, S. / Diederichs, K. / Caffrey, M. / Wang, M.
History
DepositionFeb 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _entity.formula_weight
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _refine_hist.d_res_high / _refine_hist.d_res_low

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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)27,1867
Polymers25,1561
Non-polymers2,0316
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-1 kcal/mol
Surface area11130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.757, 76.801, 98.912
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-402-

HOH

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Components

#1: Protein Phosphatidylglycerophosphatase B


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: pgpB, yodM, BSU19650 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O34349, phosphatidylglycerophosphatase
#2: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical ChemComp-WO4 / TUNGSTATE(VI)ION


Mass: 247.838 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: WO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.9 Å3/Da / Density % sol: 57.62 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 40 %(v/v) PEG-400, 100 mM HEPES pH 7 and 100 mM lithium citrate tribasic tetrahydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.21371 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.21371 Å / Relative weight: 1
ReflectionResolution: 1.79→35.614 Å / Num. obs: 39988 / % possible obs: 91.7 % / Redundancy: 2.6 % / CC1/2: 0.92 / Rrim(I) all: 0.1 / Net I/σ(I): 7.93
Reflection shellResolution: 1.79→1.9 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 0.91 / Num. unique obs: 6925 / CC1/2: 0.5 / Rrim(I) all: 1.32 / % possible all: 90

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.79→35.614 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0.85 / Phase error: 31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2624 2168 4.99 %
Rwork0.2366 --
obs0.2379 39988 90.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.79→35.614 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1579 0 124 73 1776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051754
X-RAY DIFFRACTIONf_angle_d0.8222349
X-RAY DIFFRACTIONf_dihedral_angle_d8.6081360
X-RAY DIFFRACTIONf_chiral_restr0.046266
X-RAY DIFFRACTIONf_plane_restr0.006280
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7893-1.83090.43521300.41472544X-RAY DIFFRACTION84
1.8309-1.87670.3651520.36382849X-RAY DIFFRACTION95
1.8767-1.92750.54591300.53612431X-RAY DIFFRACTION81
1.9275-1.98420.3671550.31882921X-RAY DIFFRACTION96
1.9842-2.04820.30851580.29532858X-RAY DIFFRACTION96
2.0482-2.12140.30091490.26562896X-RAY DIFFRACTION96
2.1214-2.20630.28841550.25042862X-RAY DIFFRACTION95
2.2063-2.30670.30841340.31752666X-RAY DIFFRACTION87
2.3067-2.42830.29991440.22542802X-RAY DIFFRACTION94
2.4283-2.58040.22181480.20632842X-RAY DIFFRACTION94
2.5804-2.77960.20961530.20412803X-RAY DIFFRACTION93
2.7796-3.05930.21191430.19132777X-RAY DIFFRACTION92
3.0593-3.50170.22951420.1992704X-RAY DIFFRACTION89
3.5017-4.41070.21511370.20422646X-RAY DIFFRACTION87
4.4107-38.40930.27941380.23112635X-RAY DIFFRACTION86

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