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- PDB-6chj: Wax ester synthase/diacylglycerol acyltransferase from Marinobact... -

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Basic information

Entry
Database: PDB / ID: 6chj
TitleWax ester synthase/diacylglycerol acyltransferase from Marinobacter aquaeolei VT8
ComponentsDiacylglycerol O-acyltransferase
KeywordsTRANSFERASE / WS/DGAT / wax ester synthase / diacylglycerol acyltransferase
Function / homology
Function and homology information


triglyceride biosynthetic process / diacylglycerol O-acyltransferase / diacylglycerol O-acyltransferase activity / glycerol metabolic process / response to nitric oxide / response to hypoxia / plasma membrane
Similarity search - Function
O-acyltransferase, WSD1-like, N-terminal / O-acyltransferase WSD1, C-terminal / Acyltransferase, WS/DGAT/MGAT / O-acyltransferase WSD1-like / Wax ester synthase/diacylglycerol acyltransferase catalytic domain / WS/DGAT C-terminal domain
Similarity search - Domain/homology
diacylglycerol O-acyltransferase
Similarity search - Component
Biological speciesMarinobacter hydrocarbonoclasticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.428 Å
AuthorsPetronikolou, N. / Satish, S.K.
CitationJournal: Acs Catalysis / Year: 2018
Title: Structural and Biochemical Studies of a Biocatalyst for the Enzymatic Production of Wax Esters.
Authors: Petronikolou, N. / Nair, S.K.
History
DepositionFeb 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Diacylglycerol O-acyltransferase
B: Diacylglycerol O-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,2918
Polymers103,0782
Non-polymers2136
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-70 kcal/mol
Surface area35160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.268, 103.905, 69.529
Angle α, β, γ (deg.)90.00, 103.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Diacylglycerol O-acyltransferase


Mass: 51538.910 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinobacter hydrocarbonoclasticus (strain ATCC 700491 / DSM 11845 / VT8) (bacteria)
Strain: ATCC 700491 / DSM 11845 / VT8 / Gene: Maqu_0168 / Production host: Escherichia coli (E. coli)
References: UniProt: A1TX06, diacylglycerol O-acyltransferase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.36 Å3/Da / Density % sol: 47.89 %
Crystal growTemperature: 282.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M L-Pro, 0.1 M MES, pH 7.0, 8% PEG 3350

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.428→103.9 Å / Num. obs: 36232 / % possible obs: 100 % / Redundancy: 10.8 % / Rsym value: 0.067 / Net I/σ(I): 23.4
Reflection shellResolution: 2.428→2.437 Å / Redundancy: 10.6 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 366 / CC1/2: 0.71 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
autoPROCdata scaling
PHASERphasing
autoPROCdata processing
autoPROCdata reduction
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: In-house Se-Met model

Resolution: 2.428→51.952 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.66
RfactorNum. reflection% reflection
Rfree0.2787 1803 4.98 %
Rwork0.211 --
obs0.2146 36196 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.428→51.952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6425 0 6 42 6473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086575
X-RAY DIFFRACTIONf_angle_d0.9928925
X-RAY DIFFRACTIONf_dihedral_angle_d4.3963989
X-RAY DIFFRACTIONf_chiral_restr0.05993
X-RAY DIFFRACTIONf_plane_restr0.0061157
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4284-2.49410.35931290.31032679X-RAY DIFFRACTION100
2.4941-2.56750.36281200.27022633X-RAY DIFFRACTION100
2.5675-2.65030.32351390.24882633X-RAY DIFFRACTION100
2.6503-2.74510.3331260.24162631X-RAY DIFFRACTION100
2.7451-2.8550.30681340.2422642X-RAY DIFFRACTION100
2.855-2.98490.33471460.25122635X-RAY DIFFRACTION100
2.9849-3.14220.35591240.24832652X-RAY DIFFRACTION100
3.1422-3.33910.33831380.22442631X-RAY DIFFRACTION100
3.3391-3.59680.26511490.21992642X-RAY DIFFRACTION100
3.5968-3.95870.29171460.19952631X-RAY DIFFRACTION100
3.9587-4.53120.21521480.17992651X-RAY DIFFRACTION100
4.5312-5.70770.25031630.19082643X-RAY DIFFRACTION100
5.7077-51.96440.27181410.19762690X-RAY DIFFRACTION100

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