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- PDB-7nxg: Wax synthase 1 from Acinetobacter baylyi (AbWSD1) co-crystallized... -

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Basic information

Entry
Database: PDB / ID: 7nxg
TitleWax synthase 1 from Acinetobacter baylyi (AbWSD1) co-crystallized with myristic acid
ComponentsO-acyltransferase WSD
KeywordsBIOSYNTHETIC PROTEIN / acyltransferase / wax synthase / wax synthase/acyl-CoA:diacylglycerol acyltransferase
Function / homology
Function and homology information


long-chain-alcohol O-fatty-acyltransferase / long-chain-alcohol O-fatty-acyltransferase activity / : / triglyceride biosynthetic process / diacylglycerol O-acyltransferase / diacylglycerol O-acyltransferase activity / glycerol metabolic process
Similarity search - Function
O-acyltransferase WSD1-like / O-acyltransferase, WSD1-like, N-terminal / O-acyltransferase WSD1, C-terminal / Acyltransferase, WS/DGAT/MGAT / Wax ester synthase/diacylglycerol acyltransferase catalytic domain / WS/DGAT C-terminal domain
Similarity search - Domain/homology
MYRISTIC ACID / O-acyltransferase WSD
Similarity search - Component
Biological speciesAcinetobacter baylyi ADP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsVollheyde, K. / Kuehnel, K. / Lambrecht, F. / Kawelke, S. / Herrfurth, C. / Feussner, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Acs Catalysis / Year: 2022
Title: Crystal Structure of the Bifunctional Wax Synthase 1 from Acinetobacter baylyi Suggests a Conformational Change upon Substrate Binding and Formation of Additional Substrate Binding Sites
Authors: Vollheyde, K. / Kuhnel, K. / Lambrecht, F. / Kawelke, S. / Herrfurth, C. / Feussner, I.
History
DepositionMar 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 2.0Oct 12, 2022Group: Atomic model / Database references / Source and taxonomy
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / citation_author / entity_src_gen
Item: _atom_site_anisotrop.id / _citation.country ..._atom_site_anisotrop.id / _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.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _entity_src_gen.pdbx_gene_src_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: O-acyltransferase WSD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5872
Polymers52,3581
Non-polymers2281
Water3,783210
1
A: O-acyltransferase WSD
hetero molecules

A: O-acyltransferase WSD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,1744
Polymers104,7172
Non-polymers4572
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area3640 Å2
ΔGint-15 kcal/mol
Surface area31710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.320, 118.320, 142.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

#1: Protein O-acyltransferase WSD / Diacylglycerol O-acyltransferase / DGAT / Long-chain-alcohol O-fatty-acyltransferase / Wax ester ...Diacylglycerol O-acyltransferase / DGAT / Long-chain-alcohol O-fatty-acyltransferase / Wax ester synthase/acyl-CoA:diacylglycerol acyltransferase / Wax synthase / WS


Mass: 52358.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baylyi ADP1 (bacteria) / Strain: ATCC 33305 / BD413 / ADP1 / Gene: wax-dgaT, ACIAD0832 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star
References: UniProt: Q8GGG1, diacylglycerol O-acyltransferase, long-chain-alcohol O-fatty-acyltransferase
#2: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.3848.37
2
Crystal grow
Temperature (K)Crystal-IDMethodDetails
277.151vapor diffusion, sitting dropNative crystal: Crystals were grown by in situ proteolysis with trypsin. Trypsin was added in a 1:200 (w/w) ration to 20 mg/mL native His6-TF-AbWSD1 before set up of the crystallization screens. 100 nL precipitant (17.3 % ethanol, 0.2 M MgCl2, 0.1 M TRIS pH 8.0) were added to 200 nL protein using 96-well plates with a Cartesian pipetting robot (Zinsser Analytic). Plates were stored at 277.15 K. Crystals were transferred into a cryoprotectant consisting of mother liquor supplemented with 30 % ethylene glycol and then flash cooled in liquid nitrogen.
277.152vapor diffusion, sitting dropSeMet crystal: Trypsin was added in a 1:1000 ratio (w/w) to 15 mg/mL selenomethionine-labelled His6-TF-AbWSD1. Sitting drops consisting of 100 nL protein and 100 nL precipitant (14.1 % ethanol, 0.1 M MgCl2, 0.1 M HEPES pH 7.5) were pipetted with a Gryphon robot (Art Robbins Instruments). The 96-well plates were stored at 277.15 K. For cryoprotection of the crystals, 2-methyl-2,4-pentanediol was added to the crystallization drop by transferring it five times with a 0.4 mm LithoLoop (Molecular Dimensions) at 277.15 K. Crystals were then harvested from the drop and flash-cooled in liquid nitrogen.

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21002N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X10SA10.9788
SYNCHROTRONSLS X06SA20.97644
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELMay 5, 2014
DECTRIS EIGER X 16M2PIXELMay 5, 2016
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97881
20.976441
ReflectionResolution: 1.95→44.1 Å / Num. obs: 36998 / % possible obs: 99.7 % / Redundancy: 13.172 % / Biso Wilson estimate: 39.11 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.091 / Χ2: 0.838 / Net I/σ(I): 19.91 / Num. measured all: 487337 / Scaling rejects: 52
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.95-2.0512.6992.1191.4650490.6592.20699.4
2.05-2.1513.841.0982.9242000.8771.13999.5
2.15-2.3513.6540.6035.2263610.9510.62699.6
2.35-813.0250.0630.412077210.06399.8
8-1412.8670.02285.548710.02399.8
14-1712.0730.0283.45550.9990.021100
17-5010.0950.02178.777410.02297.4

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Processing

Software
NameVersionClassification
PHENIX1.19.1refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→44.1 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2093 1850 5 %
Rwork0.1885 35135 -
obs0.1896 36985 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 183.36 Å2 / Biso mean: 50.5539 Å2 / Biso min: 26.42 Å2
Refinement stepCycle: final / Resolution: 1.95→44.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3050 0 43 210 3303
Biso mean--51.77 49.29 -
Num. residues----390
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-20.4341400.4022668280899
2-2.060.31971390.28062638277799
2.06-2.130.26541400.2532655279599
2.13-2.20.25091400.239226652805100
2.2-2.290.26861410.215626702811100
2.29-2.40.22961390.201426722811100
2.4-2.520.24821420.199926692811100
2.52-2.680.2291420.227102852100
2.68-2.890.25531420.207227042846100
2.89-3.180.2371430.193426932836100
3.18-3.640.20721440.181127412885100
3.64-4.580.15481450.145327602905100
4.58-44.10.17951530.176628903043100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.5415-0.69860.10721.3005-0.30821.0927-0.0263-0.16560.29370.2068-0.0004-0.0416-0.12050.0740.02990.3936-0.00730.01350.3367-0.0150.336943.802118.933549.0532
22.45381.0223-0.57092.4371-1.33992.37210.00610.06750.07820.05420.09070.257-0.0012-0.1601-0.08260.3298-0.00040.02970.2921-0.0120.329927.1206-1.816750.4296
36.17180.71710.28881.6532-0.64132.96690.069-0.4656-0.01870.248-0.09810.13140.07620.10.08270.45280.02710.07940.31530.00370.320535.1308-7.677358.6242
41.42450.1567-0.08793.2236-0.08150.71870.0150.04140.04470.1488-0.00610.16460.06590.00410.00430.39090.00730.02910.3693-0.00970.318829.76314.5751.0619
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -4 through 220 )A-4 - 220
2X-RAY DIFFRACTION2chain 'A' and (resid 221 through 276 )A221 - 276
3X-RAY DIFFRACTION3chain 'A' and (resid 277 through 351 )A277 - 351
4X-RAY DIFFRACTION4chain 'A' and (resid 352 through 451 )A352 - 451

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