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- PDB-7cqm: PlsY grown in LCP soaked with selenourea for 22 min -

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Basic information

Entry
Database: PDB / ID: 7cqm
TitlePlsY grown in LCP soaked with selenourea for 22 min
ComponentsGlycerol-3-phosphate acyltransferase
KeywordsTRANSFERASE / selenourea / Se-SAD / LCP / PlsY
Function / homology
Function and homology information


acyl phosphate:glycerol-3-phosphate acyltransferase / acyl-phosphate glycerol-3-phosphate acyltransferase activity / phospholipid biosynthetic process / plasma membrane
Similarity search - Function
Glycerol-3-phosphate acyltransferase, PlsY / Glycerol-3-phosphate acyltransferase / Glycerol-3-phosphate acyltransferase
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate / selenourea / Glycerol-3-phosphate acyltransferase
Similarity search - Component
Biological speciesAquifex aeolicus VF5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsLuo, Z.P. / Li, D.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Crystals / Year: 2022
Title: Selenourea for experimental phasing of membrane protein crystals grown in lipid cubic phase
Authors: Luo, Z.P. / Gu, W. / Wang, Y. / Tang, Y. / Li, D.F.
History
DepositionAug 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2022Group: 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.pdbx_database_id_DOI / _citation.year / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycerol-3-phosphate acyltransferase
B: Glycerol-3-phosphate acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,63947
Polymers43,7282
Non-polymers8,91145
Water2,162120
1
A: Glycerol-3-phosphate acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,70925
Polymers21,8641
Non-polymers4,84524
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint-41 kcal/mol
Surface area10560 Å2
MethodPISA
2
B: Glycerol-3-phosphate acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,92922
Polymers21,8641
Non-polymers4,06521
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint-42 kcal/mol
Surface area10550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.877, 88.990, 53.982
Angle α, β, γ (deg.)90.000, 95.190, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glycerol-3-phosphate acyltransferase / Acyl-PO4 G3P acyltransferase / Acyl-phosphate--glycerol-3-phosphate acyltransferase / G3P ...Acyl-PO4 G3P acyltransferase / Acyl-phosphate--glycerol-3-phosphate acyltransferase / G3P acyltransferase / GPAT / Lysophosphatidic acid synthase / LPA synthase


Mass: 21863.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Strain: VF5 / Gene: plsY, aq_676 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O66905, acyl phosphate:glycerol-3-phosphate acyltransferase
#2: Chemical
ChemComp-SEY / selenourea / Selenourea


Mass: 123.016 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: CH4N2Se / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-79M / (2R)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate / [(2R)-2,3-bis(oxidanyl)propyl] (Z)-hexadec-7-enoate


Mass: 328.487 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C19H36O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.95 Å3/Da / Density % sol: 58.27 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 25-35% (v/v) triethylene glycol, 0.1 M ammonium sulfate, 0.1 M glycine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97907 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.564
11-L, -K, -H20.436
ReflectionResolution: 1.8→50 Å / Num. obs: 46884 / % possible obs: 99.6 % / Redundancy: 6.7 % / CC1/2: 1 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.039 / Net I/σ(I): 1.69
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.973 / Mean I/σ(I) obs: 18.59 / Num. unique obs: 4730 / CC1/2: 0.687 / Rpim(I) all: 0.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→36.37 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.269 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.024 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1902 2070 4.9 %RANDOM
Rwork0.1564 ---
obs0.158 40046 89.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 108.92 Å2 / Biso mean: 25.337 Å2 / Biso min: 9.09 Å2
Baniso -1Baniso -2Baniso -3
1-8.34 Å20 Å23.92 Å2
2---10.31 Å2-0 Å2
3---1.97 Å2
Refinement stepCycle: final / Resolution: 1.8→36.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3062 0 497 120 3679
Biso mean--51.37 30.8 -
Num. residues----400
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0143601
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163711
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.664768
X-RAY DIFFRACTIONr_angle_other_deg0.4381.7848495
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6455400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.81619.516124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.55815490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0961516
X-RAY DIFFRACTIONr_chiral_restr0.0770.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0540.023818
X-RAY DIFFRACTIONr_gen_planes_other0.0450.02842
X-RAY DIFFRACTIONr_mcbond_it3.5844.0331603
X-RAY DIFFRACTIONr_mcbond_other3.534.0311602
X-RAY DIFFRACTIONr_mcangle_it4.3947.5362002
LS refinement shellResolution: 1.8→1.845 Å
RfactorNum. reflection% reflection
Rfree0.264 98 -
Rwork0.189 1355 -
obs--42.15 %

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