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- PDB-7b0q: In meso structure of the membrane integral lipoprotein intramolec... -

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Basic information

Entry
Database: PDB / ID: 7b0q
TitleIn meso structure of the membrane integral lipoprotein intramolecular transacylase Lit from Bacillus cereus with H85A mutation
ComponentsHypothetical Membrane Spanning Protein
KeywordsMEMBRANE PROTEIN / lipoprotein / lipid cubic phase / Lit / transacylase
Function / homologyIntegral membrane protein 1906 / Lipoprotein intramolecular transacylase Lit / 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: 2.42 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)30,90814
Polymers27,5741
Non-polymers3,33513
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint9 kcal/mol
Surface area13830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.236, 45.140, 70.174
Angle α, β, γ (deg.)90.000, 121.380, 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: 27573.727 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 , 5 types, 34 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.: 7 / Source method: obtained synthetically / Formula: C21H40O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.83 Å3/Da / Density % sol: 56.47 %
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: 0.96863 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 2.42→49.19 Å / Num. obs: 8396 / % possible obs: 92 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rrim(I) all: 0.12 / Net I/σ(I): 9.7
Reflection shellResolution: 2.42→2.64 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 420 / CC1/2: 0.518 / Rrim(I) all: 1.62 / % possible all: 66.6

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
autoPROCdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7B0O

7b0o


Resolution: 2.42→49.19 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.241 421 5.02 %
Rwork0.2185 7967 -
obs0.2197 8388 70.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.9 Å2 / Biso mean: 64.4414 Å2 / Biso min: 17.32 Å2
Refinement stepCycle: final / Resolution: 2.42→49.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1788 0 229 21 2038
Biso mean--80.09 51.82 -
Num. residues----220
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.42-2.780.288480.296788993724
2.78-3.50.30531600.26823259341987
3.5-49.190.21882130.196638194032100

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