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- PDB-7b0o: In meso structure of the membrane integral lipoprotein intramolec... -

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Basic information

Entry
Database: PDB / ID: 7b0o
TitleIn meso structure of the membrane integral lipoprotein intramolecular transacylase Lit from Bacillus cereus in space group P21
ComponentsHypothetical Membrane Spanning Protein
KeywordsMEMBRANE PROTEIN / lipoprotein / lipid cubic phase / Lit / transacylase
Function / homologyIntegral membrane protein 1906 / Lipoprotein intramolecular transacylase Lit / membrane / (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 / SAD / Resolution: 2.33 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 1.2May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
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
B: Hypothetical Membrane Spanning Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,87926
Polymers55,2822
Non-polymers5,59824
Water77543
1
A: Hypothetical Membrane Spanning Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,63913
Polymers27,6411
Non-polymers2,99812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical Membrane Spanning Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,24013
Polymers27,6411
Non-polymers2,60012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.724, 44.700, 116.865
Angle α, β, γ (deg.)90.000, 92.380, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Hypothetical Membrane Spanning Protein


Mass: 27640.795 Da / Num. of mol.: 2
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 , 5 types, 67 molecules

#2: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C21H40O4 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE


Mass: 178.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O4
#6: 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.5765.5
23.5765.5
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.6
Details: 100 mM sodium citrate/HCl, pH 5.6, 40 %(v/v) polyethylene glycol (PEG) 400, 100 mM ammonium sulfate, and 200 mM sodium formate

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21002N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I2410.96862
SYNCHROTRONSLS X06SA20.97793
Detector
TypeIDDetectorDate
DECTRIS PILATUS3 6M1PIXELDec 1, 2018
DECTRIS EIGER X 16M2PIXELFeb 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.968621
20.977931
ReflectionResolution: 2.27→67.76 Å / Num. obs: 24031 / % possible obs: 91.5 % / Redundancy: 6.2 % / CC1/2: 0.96 / Rrim(I) all: 0.29 / Net I/σ(I): 3.4
Reflection shellResolution: 2.27→2.45 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1202 / CC1/2: 0.18 / Rrim(I) all: 1.45 / % possible all: 56.6

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing
BUCCANEERmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.33→43.32 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2873 979 4.99 %
Rwork0.2451 18626 -
obs0.2472 19605 64.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 151.41 Å2 / Biso mean: 54.2705 Å2 / Biso min: 5.66 Å2
Refinement stepCycle: final / Resolution: 2.33→43.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3494 0 374 43 3911
Biso mean--69.11 43.08 -
Num. residues----427
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.33-2.450.4348220.302843545711
2.45-2.60.3491770.30911321139833
2.6-2.810.33571050.28652214231954
2.81-3.090.32131570.2772972312973
3.09-3.530.30592050.26263757396291
3.53-4.450.2782110.21943951416295
4.45-43.320.25992020.23613976417893
Refinement TLS params.Method: refined / Origin x: 12.9933 Å / Origin y: -5.232 Å / Origin z: 30.0965 Å
111213212223313233
T-0.0991 Å20.0469 Å20.0266 Å2--0.2728 Å2-0.4699 Å2---0.3219 Å2
L0.0262 °20.1177 °20.1659 °2-0.4383 °20.1931 °2--0.9648 °2
S-0.068 Å °0.1264 Å °0.006 Å °-0.1932 Å °-0.2026 Å °-0.4489 Å °0.0505 Å °0.8088 Å °-2.0762 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-6 - 1101
2X-RAY DIFFRACTION1allA1201 - 1301
3X-RAY DIFFRACTION1allB-1 - 1701
4X-RAY DIFFRACTION1allB1801 - 2001
5X-RAY DIFFRACTION1allC1 - 52

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