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- PDB-7b0p: In meso structure of the membrane integral lipoprotein intramolec... -

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Basic information

Entry
Database: PDB / ID: 7b0p
TitleIn meso structure of the membrane integral lipoprotein intramolecular transacylase Lit from Bacillus cereus in space group P21212
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 / MOLECULAR REPLACEMENT / Resolution: 1.935 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
B: Hypothetical Membrane Spanning Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,12030
Polymers55,2822
Non-polymers5,83828
Water3,027168
1
A: Hypothetical Membrane Spanning Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,43717
Polymers27,6411
Non-polymers2,79616
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical Membrane Spanning Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,68313
Polymers27,6411
Non-polymers3,04212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.166, 192.235, 76.801
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid -2 through 17 or resid 19 through 212 or resid 2601 through 3001))
21(chain B and (resid -2 through 17 or resid 19 through 212 or resid 1901 through 2301))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid -2 through 17 or resid 19 through 212 or resid 2601 through 3001))A-2 - 17
121(chain A and (resid -2 through 17 or resid 19 through 212 or resid 2601 through 3001))A19 - 212
131(chain A and (resid -2 through 17 or resid 19 through 212 or resid 2601 through 3001))A2601 - 3001
211(chain B and (resid -2 through 17 or resid 19 through 212 or resid 1901 through 2301))B-2 - 17
221(chain B and (resid -2 through 17 or resid 19 through 212 or resid 1901 through 2301))B19 - 212
231(chain B and (resid -2 through 17 or resid 19 through 212 or resid 1901 through 2301))B1901 - 2301

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Components

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


Mass: 356.540 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C21H40O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
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: 3.42 Å3/Da / Density % sol: 63.99 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.5
Details: 100 mM sodium citrate/HCl, pH 5.5, 75-150 mM NaCl, and 36-44 %(v/v) PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.935→60 Å / Num. obs: 29001 / % possible obs: 89.5 % / Redundancy: 5.4 % / CC1/2: 0.73 / Rrim(I) all: 0.66 / Net I/σ(I): 4.4
Reflection shellResolution: 1.94→2.28 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1451 / CC1/2: 0.162 / Rrim(I) all: 6.07 / % possible all: 47.4

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_3494refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
autoPROCdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7B0O

7b0o


Resolution: 1.935→60 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2462 1443 5.18 %
Rwork0.2322 26394 -
obs0.2329 27837 48.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.08 Å2 / Biso mean: 34.3226 Å2 / Biso min: 3.84 Å2
Refinement stepCycle: final / Resolution: 1.935→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3595 0 400 168 4163
Biso mean--56.32 33.51 -
Num. residues----439
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1997X-RAY DIFFRACTION13.111TORSIONAL
12B1997X-RAY DIFFRACTION13.111TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9352-2.00440.748120.532681
2.0044-2.08460.369780.39831333
2.0846-2.17950.4433120.32022374
2.1795-2.29440.2627440.333176914
2.2944-2.43820.3291820.2946150328
2.4382-2.62650.29791470.2875277251
2.6265-2.89080.30762180.2678442781
2.8908-3.3090.27042980.2482537698
3.309-4.16890.21233250.25489100
4.1689-600.22213070.2124562097
Refinement TLS params.Method: refined / Origin x: -18.3228 Å / Origin y: 28.5323 Å / Origin z: -28.3655 Å
111213212223313233
T0.0746 Å2-0.0808 Å20.0133 Å2-0.0519 Å20.0763 Å2--0.0899 Å2
L0.1547 °2-0.0961 °20.0062 °2-0.3055 °20.326 °2--1.2543 °2
S0.0262 Å °-0.0321 Å °-0.0453 Å °0.2399 Å °0.0343 Å °-0.027 Å °0.6521 Å °-0.0786 Å °0.0437 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-9 - 3201
2X-RAY DIFFRACTION1allB-2 - 2701
3X-RAY DIFFRACTION1allC1 - 188

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