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- PDB-7ojt: Crystal structure of unliganded PatA, a membrane associated acylt... -

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Basic information

Entry
Database: PDB / ID: 7ojt
TitleCrystal structure of unliganded PatA, a membrane associated acyltransferase from Mycobacterium smegmatis
ComponentsPhosphatidylinositol mannoside acyltransferase
KeywordsTRANSFERASE / Acyltrasnferase / Mycobacteria / integral membrane protein TRANSFERASE
Function / homologyphosphatidylinositol dimannoside acyltransferase / Bacterial lipid A biosynthesis acyltransferase / Bacterial lipid A biosynthesis acyltransferase / glycolipid biosynthetic process / phospholipid biosynthetic process / phosphatidylinositol metabolic process / acyltransferase activity / plasma membrane / Phosphatidylinositol mannoside acyltransferase
Function and homology information
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.67 Å
AuthorsAnso, I. / Wang, L. / Marina, A. / Paez-Perez, E.D. / Perrone, S. / Lowary, T.L. / Trastoy, B. / Guerin, M.E.
CitationJournal: Sci Adv / Year: 2021
Title: Molecular ruler mechanism and interfacial catalysis of the integral membrane acyltransferase PatA.
Authors: Anso, I. / Basso, L.G.M. / Wang, L. / Marina, A. / Paez-Perez, E.D. / Jager, C. / Gavotto, F. / Tersa, M. / Perrone, S. / Contreras, F.X. / Prandi, J. / Gilleron, M. / Linster, C.L. / ...Authors: Anso, I. / Basso, L.G.M. / Wang, L. / Marina, A. / Paez-Perez, E.D. / Jager, C. / Gavotto, F. / Tersa, M. / Perrone, S. / Contreras, F.X. / Prandi, J. / Gilleron, M. / Linster, C.L. / Corzana, F. / Lowary, T.L. / Trastoy, B. / Guerin, M.E.
History
DepositionMay 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 3, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphatidylinositol mannoside acyltransferase
B: Phosphatidylinositol mannoside acyltransferase
C: Phosphatidylinositol mannoside acyltransferase
D: Phosphatidylinositol mannoside acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,1455
Polymers139,0534
Non-polymers921
Water00
1
A: Phosphatidylinositol mannoside acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8552
Polymers34,7631
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphatidylinositol mannoside acyltransferase


Theoretical massNumber of molelcules
Total (without water)34,7631
Polymers34,7631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Phosphatidylinositol mannoside acyltransferase


Theoretical massNumber of molelcules
Total (without water)34,7631
Polymers34,7631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Phosphatidylinositol mannoside acyltransferase


Theoretical massNumber of molelcules
Total (without water)34,7631
Polymers34,7631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.310, 92.970, 81.090
Angle α, β, γ (deg.)90.000, 90.330, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 50 through 53 or (resid 54...
21(chain B and (resid 50 through 53 or (resid 54...
31(chain C and (resid 50 through 56 or (resid 57...
41(chain D and (resid 50 through 53 or (resid 54...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 50 through 53 or (resid 54...A50 - 53
121(chain A and (resid 50 through 53 or (resid 54...A54 - 55
131(chain A and (resid 50 through 53 or (resid 54...A50 - 298
141(chain A and (resid 50 through 53 or (resid 54...A50 - 298
151(chain A and (resid 50 through 53 or (resid 54...A50 - 298
161(chain A and (resid 50 through 53 or (resid 54...A50 - 298
211(chain B and (resid 50 through 53 or (resid 54...B50 - 53
221(chain B and (resid 50 through 53 or (resid 54...B54 - 55
231(chain B and (resid 50 through 53 or (resid 54...B50 - 298
241(chain B and (resid 50 through 53 or (resid 54...B50 - 298
251(chain B and (resid 50 through 53 or (resid 54...B50 - 298
261(chain B and (resid 50 through 53 or (resid 54...B57 - 59
271(chain B and (resid 50 through 53 or (resid 54...B50 - 298
281(chain B and (resid 50 through 53 or (resid 54...B50 - 298
291(chain B and (resid 50 through 53 or (resid 54...B50 - 298
2101(chain B and (resid 50 through 53 or (resid 54...B50 - 298
311(chain C and (resid 50 through 56 or (resid 57...C50 - 56
321(chain C and (resid 50 through 56 or (resid 57...C57 - 59
331(chain C and (resid 50 through 56 or (resid 57...C50 - 298
341(chain C and (resid 50 through 56 or (resid 57...C50 - 298
351(chain C and (resid 50 through 56 or (resid 57...C50 - 298
361(chain C and (resid 50 through 56 or (resid 57...C50 - 298
411(chain D and (resid 50 through 53 or (resid 54...D50 - 53
421(chain D and (resid 50 through 53 or (resid 54...D54 - 55
431(chain D and (resid 50 through 53 or (resid 54...D50 - 298
441(chain D and (resid 50 through 53 or (resid 54...D50 - 298
451(chain D and (resid 50 through 53 or (resid 54...D50 - 298
461(chain D and (resid 50 through 53 or (resid 54...D50 - 298
471(chain D and (resid 50 through 53 or (resid 54...D0
481(chain D and (resid 50 through 53 or (resid 54...D50 - 298
491(chain D and (resid 50 through 53 or (resid 54...D50 - 298
4101(chain D and (resid 50 through 53 or (resid 54...D50 - 298
4111(chain D and (resid 50 through 53 or (resid 54...D50 - 298
4121(chain D and (resid 50 through 53 or (resid 54...D50 - 298

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Components

#1: Protein
Phosphatidylinositol mannoside acyltransferase / PIM acyltransferase


Mass: 34763.340 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_2934, MSMEI_2860
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QWG5, phosphatidylinositol dimannoside acyltransferase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
Has ligand of interestN

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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: 2.21 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM imidazole/MES monohydrate pH 8.5, 60 mM divalent cations mixture (Magnesium chloride hexahydrate and calcium chloride dihydrate) and 50% (w/v) of precipitant mix based on 20% (w/v) ...Details: 100 mM imidazole/MES monohydrate pH 8.5, 60 mM divalent cations mixture (Magnesium chloride hexahydrate and calcium chloride dihydrate) and 50% (w/v) of precipitant mix based on 20% (w/v) PEG 4000 and 40% (w/v) glycerol (Morpheus protein crystallization screen)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.67→46.48 Å / Num. obs: 90742 / % possible obs: 99.07 % / Redundancy: 6.8 % / Biso Wilson estimate: 125.8 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.1792 / Rpim(I) all: 0.07376 / Rrim(I) all: 0.194 / Net I/σ(I): 9.96
Reflection shellResolution: 3.67→3.8 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.459 / Mean I/σ(I) obs: 1.41 / Num. unique obs: 7983 / CC1/2: 0.7 / CC star: 0.908 / Rpim(I) all: 0.6112 / % possible all: 94.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F2Z

5f2z


Resolution: 3.67→46.48 Å / SU ML: 0.57 / Cross valid method: THROUGHOUT / σ(F): 1.29 / Phase error: 35.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2903 1271 4.96 %
Rwork0.2676 24370 -
obs0.2689 25641 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 189.08 Å2 / Biso mean: 124.5706 Å2 / Biso min: 67.53 Å2
Refinement stepCycle: final / Resolution: 3.67→46.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7120 0 14 0 7134
Biso mean--134.55 --
Num. residues----996
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2984X-RAY DIFFRACTION7.483TORSIONAL
12B2984X-RAY DIFFRACTION7.483TORSIONAL
13C2984X-RAY DIFFRACTION7.483TORSIONAL
14D2984X-RAY DIFFRACTION7.483TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.67-3.820.42911340.3611259995
3.82-3.990.34891410.33962746100
3.99-4.20.31881450.312703100
4.2-4.470.32491390.28972714100
4.47-4.810.28091420.2567273499
4.81-5.30.30061420.2739268699
5.3-6.060.33851450.27872749100
6.06-7.630.25581410.25582726100
7.63-46.480.2351420.212271399

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