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- PDB-6a1k: Phosphate acyltransferase PlsX from B.subtilis -

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Basic information

Entry
Database: PDB / ID: 6a1k
TitlePhosphate acyltransferase PlsX from B.subtilis
ComponentsPhosphate acyltransferase
KeywordsTRANSFERASE / Phosphate acyltransferase
Function / homology
Function and homology information


phosphate acyltransferase / phosphate:acyl-[acyl carrier protein] acyltransferase activity / phospholipid biosynthetic process / fatty acid biosynthetic process / cytoplasm
Similarity search - Function
Fatty acid synthesis PlsX protein / Phospholipid biosynthesis protein, PlsX-like / Fatty acid synthesis protein / Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphate acyltransferase
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsGuo, Z. / Jiang, Y.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
Other governmentHKUST_621/13 Hong Kong
CitationJournal: Commun Biol / Year: 2019
Title: Identification of an amphipathic peptide sensor of the Bacillus subtilisfluid membrane microdomains.
Authors: Jiang, Y. / Dai, X. / Qin, M. / Guo, Z.
History
DepositionJun 7, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / citation_author
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 1.2Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphate acyltransferase
B: Phosphate acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2254
Polymers72,0332
Non-polymers1922
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-67 kcal/mol
Surface area25210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.520, 144.760, 84.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-580-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 14 or (resid 15...
21(chain B and (resid 1 through 47 or (resid 48...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETPROPRO(chain A and (resid 1 through 14 or (resid 15...AA1 - 141 - 14
12LYSLYSLYSLYS(chain A and (resid 1 through 14 or (resid 15...AA1515
13METMETVALVAL(chain A and (resid 1 through 14 or (resid 15...AA1 - 3261 - 326
14METMETVALVAL(chain A and (resid 1 through 14 or (resid 15...AA1 - 3261 - 326
15METMETVALVAL(chain A and (resid 1 through 14 or (resid 15...AA1 - 3261 - 326
16METMETVALVAL(chain A and (resid 1 through 14 or (resid 15...AA1 - 3261 - 326
21METMETTHRTHR(chain B and (resid 1 through 47 or (resid 48...BB1 - 471 - 47
22THRTHRTHRTHR(chain B and (resid 1 through 47 or (resid 48...BB48 - 4948 - 49
23METMETGLUGLU(chain B and (resid 1 through 47 or (resid 48...BB1 - 3251 - 325
24METMETGLUGLU(chain B and (resid 1 through 47 or (resid 48...BB1 - 3251 - 325
25METMETGLUGLU(chain B and (resid 1 through 47 or (resid 48...BB1 - 3251 - 325
26METMETGLUGLU(chain B and (resid 1 through 47 or (resid 48...BB1 - 3251 - 325

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Components

#1: Protein Phosphate acyltransferase / Acyl-ACP phosphotransacylase / Acyl-[acyl-carrier-protein]--phosphate acyltransferase / Phosphate- ...Acyl-ACP phosphotransacylase / Acyl-[acyl-carrier-protein]--phosphate acyltransferase / Phosphate-acyl-ACP acyltransferase


Mass: 36016.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168 / Gene: plsX, ylpD, BSU15890 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3)
References: UniProt: P71018, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O

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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: 2.38 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.08 M Tris 8.0, 0.16 M Li2SO4, 21% PEG 4000, 0.012 mM CYMAL 7, 5 % t-butanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→33.29 Å / Num. obs: 29907 / % possible obs: 96.2 % / Redundancy: 6.4 % / Biso Wilson estimate: 26.66 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.062 / Rrim(I) all: 0.118 / Net I/σ(I): 11.5
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2564 / CC1/2: 0.929 / Rpim(I) all: 0.273 / Rrim(I) all: 0.51 / % possible all: 90.9

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementResolution: 2.3→33.288 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2376 1998 6.93 %
Rwork0.2018 26831 -
obs0.2043 28829 95.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.16 Å2 / Biso mean: 31.6819 Å2 / Biso min: 8.33 Å2
Refinement stepCycle: final / Resolution: 2.3→33.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4617 0 10 259 4886
Biso mean--72.95 36.86 -
Num. residues----651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074680
X-RAY DIFFRACTIONf_angle_d0.9766370
X-RAY DIFFRACTIONf_chiral_restr0.054799
X-RAY DIFFRACTIONf_plane_restr0.009825
X-RAY DIFFRACTIONf_dihedral_angle_d11.3383319
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2678X-RAY DIFFRACTION10.821TORSIONAL
12B2678X-RAY DIFFRACTION10.821TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.35750.26321310.21531755188690
2.3575-2.42130.31021320.22241781191391
2.4213-2.49250.27841360.23411825196192
2.4925-2.57290.25461370.22671846198394
2.5729-2.66480.26741430.241912205596
2.6648-2.77150.30571410.23931900204198
2.7715-2.89750.27811470.24121974212199
2.8975-3.05020.30511460.24371965211199
3.0502-3.24120.22291470.22361972211999
3.2412-3.49120.23181470.20351973212099
3.4912-3.8420.22381480.18071983213199
3.842-4.39690.20631450.16171950209597
4.3969-5.53550.19431440.16641920206494
5.5355-33.29140.20391540.19082075222997
Refinement TLS params.Method: refined / Origin x: 27.9069 Å / Origin y: 6.5844 Å / Origin z: 20.3418 Å
111213212223313233
T0.0698 Å20.0208 Å2-0.0079 Å2-0.0904 Å20.0351 Å2--0.0819 Å2
L0.1066 °20.1454 °2-0.0818 °2-0.2646 °2-0.0186 °2--0.2684 °2
S0.014 Å °-0.0679 Å °-0.0101 Å °-0.0087 Å °-0.0019 Å °-0.0792 Å °0.0374 Å °-0.0478 Å °0.0147 Å °
Refinement TLS groupSelection details: all

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