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- PDB-7b0r: In meso structure of the membrane integral lipoprotein intramolec... -

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Basic information

Entry
Database: PDB / ID: 7b0r
TitleIn meso structure of the membrane integral lipoprotein intramolecular transacylase Lit from Bacillus cereus with H85R mutation
ComponentsHypothetical Membrane Spanning Protein
KeywordsMEMBRANE PROTEIN / lipoprotein / lipid cubic phase / Lit / transacylase
Function / homologyIntegral membrane protein 1906 / Protein of unknown function (DUF1461) / membrane / CITRIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / Hypothetical Membrane Spanning Protein
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHuang, C.-Y. / Olatunji, S. / Olieric, V. / Caffrey, M.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland16/IA/4435 Ireland
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis of the membrane intramolecular transacylase reaction responsible for lyso-form lipoprotein synthesis.
Authors: Olatunji, S. / Bowen, K. / Huang, C.Y. / Weichert, D. / Singh, W. / Tikhonova, I.G. / Scanlan, E.M. / Olieric, V. / Caffrey, M.
History
DepositionNov 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: 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: Hypothetical Membrane Spanning Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,13111
Polymers27,6601
Non-polymers2,47110
Water77543
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint7 kcal/mol
Surface area14110 Å2
Unit cell
Length a, b, c (Å)114.472, 44.871, 69.543
Angle α, β, γ (deg.)90.000, 121.060, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Hypothetical Membrane Spanning Protein


Mass: 27659.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711) (bacteria)
Strain: ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711
Gene: BC_1526 / Production host: Escherichia coli (E. coli) / References: UniProt: Q813T3

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Non-polymers , 6 types, 53 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H40O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400


Mass: 398.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#5: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#6: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE


Mass: 178.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.77 Å3/Da / Density % sol: 55.53 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100 mM MES/NaOH, pH 6.0, 125-200 mM M lithium citrate tribasic tetrahydrate, and 36-44 %(v/v) PEG 400
PH range: 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 2.2→40.8 Å / Num. obs: 14531 / % possible obs: 92.6 % / Redundancy: 6.48 % / CC1/2: 0.99 / Rrim(I) all: 0.15 / Net I/σ(I): 10.46
Reflection shellResolution: 2.2→2.33 Å / Mean I/σ(I) obs: 1.23 / Num. unique obs: 1674 / CC1/2: 0.64 / Rrim(I) all: 1.42

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Processing

Software
NameVersionClassification
PHENIX1.17.1-3660refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7B0O

7b0o


Resolution: 2.2→40.8 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.28 --
Rwork0.23 --
obs-14504 100 %
Displacement parametersBiso max: 124.59 Å2 / Biso mean: 55.0676 Å2 / Biso min: 23.29 Å2
Refinement stepCycle: LAST / Resolution: 2.2→40.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1824 0 161 43 2028

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