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- PDB-1vi1: Crystal structure of a fatty acid/phospholipid synthesis protein -

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Basic information

Entry
Database: PDB / ID: 1vi1
TitleCrystal structure of a fatty acid/phospholipid synthesis protein
ComponentsFatty acid/phospholipid synthesis protein plsX
KeywordsStructural genomics / unknown function
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Se-Met MAD phasing / Resolution: 2.95 Å
AuthorsStructural GenomiX
CitationJournal: Proteins / Year: 2005
Title: Structural analysis of a set of proteins resulting from a bacterial genomics project
Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / ...Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / Feil, I. / Furlong, E.B. / Gajiwala, K.S. / Gao, X. / He, D. / Hendle, J. / Huber, A. / Hoda, K. / Kearins, P. / Kissinger, C. / Laubert, B. / Lewis, H.A. / Lin, J. / Loomis, K. / Lorimer, D. / Louie, G. / Maletic, M. / Marsh, C.D. / Miller, I. / Molinari, J. / Muller-Dieckmann, H.J. / Newman, J.M. / Noland, B.W. / Pagarigan, B. / Park, F. / Peat, T.S. / Post, K.W. / Radojicic, S. / Ramos, A. / Romero, R. / Rutter, M.E. / Sanderson, W.E. / Schwinn, K.D. / Tresser, J. / Winhoven, J. / Wright, T.A. / Wu, L. / Xu, J. / Harris, T.J.
History
DepositionDec 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fatty acid/phospholipid synthesis protein plsX
B: Fatty acid/phospholipid synthesis protein plsX


Theoretical massNumber of molelcules
Total (without water)75,5902
Polymers75,5902
Non-polymers00
Water724
1
A: Fatty acid/phospholipid synthesis protein plsX


Theoretical massNumber of molelcules
Total (without water)37,7951
Polymers37,7951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fatty acid/phospholipid synthesis protein plsX


Theoretical massNumber of molelcules
Total (without water)37,7951
Polymers37,7951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Fatty acid/phospholipid synthesis protein plsX

B: Fatty acid/phospholipid synthesis protein plsX


Theoretical massNumber of molelcules
Total (without water)75,5902
Polymers75,5902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
Buried area3480 Å2
ΔGint-41 kcal/mol
Surface area26370 Å2
MethodPISA, PQS
4
A: Fatty acid/phospholipid synthesis protein plsX

A: Fatty acid/phospholipid synthesis protein plsX


Theoretical massNumber of molelcules
Total (without water)75,5902
Polymers75,5902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
Buried area3530 Å2
ΔGint-41 kcal/mol
Surface area27240 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)170.314, 170.314, 187.838
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Fatty acid/phospholipid synthesis protein plsX


Mass: 37795.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: PLSX, BSU15890 / Production host: Escherichia coli (E. coli) / References: UniProt: P71018
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.47 Å3/Da / Density % sol: 64.53 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMHEPES1droppH7.5
2150 mM1dropNaCl
310 mMmethionine1drop
410 %glycerol1drop
55 mMdithiothreitol1drop
610 mg/mlprotein1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.9795, 0.9641
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: MAD / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.96411
ReflectionResolution: 2.82→47.94 Å / Num. all: 25534 / Num. obs: 25534 / % possible obs: 85.7 % / Redundancy: 11.46 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 15.5
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 2.2
Reflection
*PLUS
Redundancy: 11.5 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMAC4refinement
RefinementMethod to determine structure: Se-Met MAD phasing / Resolution: 2.95→47.94 Å / σ(F): 0
RfactorNum. reflection
Rfree0.334 1116
Rwork0.285 -
obs-22217
Solvent computationSolvent model: Babinet bulk solvent correction / Bsol: 158.908 Å2 / ksol: 0.821 e/Å3
Displacement parametersBiso mean: 64.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.777 Å20.389 Å20 Å2
2--0.777 Å20 Å2
3----1.166 Å2
Refine Biso Class: all / Treatment: isotropic
Refinement stepCycle: LAST / Resolution: 2.95→47.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4756 0 0 4 4760
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_d2.433
X-RAY DIFFRACTIONp_planar_tor2.261
X-RAY DIFFRACTIONp_chiral_restr0.147
X-RAY DIFFRACTIONp_plane_restr0.02
X-RAY DIFFRACTIONp_mcbond_it2.062
X-RAY DIFFRACTIONp_mcangle_it3.803
X-RAY DIFFRACTIONp_scbond_it3.891
X-RAY DIFFRACTIONp_scangle_it6.219
Software
*PLUS
Version: 4 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.4

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