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- PDB-7t63: Crystal structure of a delta 6 18:0-ACP desaturase from Thunbergi... -

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Entry
Database: PDB / ID: 7t63
TitleCrystal structure of a delta 6 18:0-ACP desaturase from Thunbergia laurifolia
ComponentsDESATURASE
KeywordsOXIDOREDUCTASE / DELTA6 FATTY ACID DESATURASE / BINUCLEAR IRON CENTER / ELECTRON TRANSFER
Function / homology:
Function and homology information
Biological speciesThunbergia laurifolia (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLiu, Q. / Chai, J. / Shanklin, J.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Divergent evolution of extreme production of variant plant monounsaturated fatty acids.
Authors: Gan, L. / Park, K. / Chai, J. / Updike, E.M. / Kim, H. / Voshall, A. / Behera, S. / Yu, X.H. / Cai, Y. / Zhang, C. / Wilson, M.A. / Mower, J.P. / Moriyama, E.N. / Zhang, C. / Kaewsuwan, S. / ...Authors: Gan, L. / Park, K. / Chai, J. / Updike, E.M. / Kim, H. / Voshall, A. / Behera, S. / Yu, X.H. / Cai, Y. / Zhang, C. / Wilson, M.A. / Mower, J.P. / Moriyama, E.N. / Zhang, C. / Kaewsuwan, S. / Liu, Q. / Shanklin, J. / Cahoon, E.B.
History
DepositionDec 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DESATURASE
B: DESATURASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,1596
Polymers78,9352
Non-polymers2234
Water9,350519
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-69 kcal/mol
Surface area25230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.896, 129.700, 62.996
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 23 through 356)
d_2ens_1(chain "B" and (resid 23 through 331 or resid 340 through 341 or resid 344 through 356))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ARGVALA2 - 325
d_21ens_1ARGARGB1 - 309
d_22ens_1ALAGLUB318 - 319
d_23ens_1SERVALB322 - 334

NCS oper: (Code: givenMatrix: (-0.118476228695, 0.301506663052, -0.94607458235), (0.295683112082, -0.898848903108, -0.323484383876), (-0.947910797736, -0.318063486614, 0.0173417997618)Vector: 115. ...NCS oper: (Code: given
Matrix: (-0.118476228695, 0.301506663052, -0.94607458235), (0.295683112082, -0.898848903108, -0.323484383876), (-0.947910797736, -0.318063486614, 0.0173417997618)
Vector: 115.527113547, 50.5116193258, 123.529016125)

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Components

#1: Protein DESATURASE


Mass: 39467.691 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thunbergia laurifolia (plant) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 519 / 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: 2.73 Å3/Da / Density % sol: 54.92 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop
Details: 0.1M BICINE, 2-4% v/v 1,4-Dioxane, 10% w/v Polyethylene glycol 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 1.74333 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.74333 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 90410 / % possible obs: 84.6 % / Redundancy: 7.6 % / Biso Wilson estimate: 28.03 Å2 / CC1/2: 0.996 / Net I/σ(I): 10.5
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 1389 / CC1/2: 0.576

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AFR

1afr


Resolution: 2→39.82 Å / SU ML: 0.2209 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.6433
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2258 4580 5.07 %
Rwork0.2076 85830 -
obs0.2085 90410 83.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.15 Å2
Refinement stepCycle: LAST / Resolution: 2→39.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5304 0 4 520 5828
Refine LS restraintsType: f_dihedral_angle_d / Dev ideal: 17.2159 / Number: 2022
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.14829727196 Å
LS refinement shellResolution: 2→2.02 Å
RfactorNum. reflection% reflection
Rfree0.4421 57 -
Rwork0.4241 970 -
obs--28.26 %
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)
11.91740833579-0.453381345574-0.0679468253811.796001910290.4299115071551.7408049190.03512866074590.2580971991430.552120432213-0.118419207311-0.0447436283645-0.508751300133-0.2889661401020.420289476615-0.04039378938940.330807323091-0.007011753433510.007063800418920.4067950509390.04749915866850.28767887164681.420283079933.296379016315.8177964481
20.1796865177410.3183181938810.0141101531020.5454855814960.108095520231.670786694330.0753736604507-0.02424782708120.006976126180920.0228403458427-0.0670158449720.167512600972-0.0591222579734-0.2652805887630.02898207304080.2534763386090.000984740953514-0.02646977046670.28833379144-0.007859074098550.25478346222659.473312994133.238912775439.7083978521
32.07001929198-2.04173498539-1.207123521626.061954610672.708228674552.93632696841-0.2764557847450.269107256035-0.6395183829250.600121169937-0.2000213528181.175893560740.605083156774-0.7360137115450.3632499974240.30874351123-0.1202703715860.04654539218450.3561250733730.03274645151390.4259355066256.252234179118.455468375754.7986137554
40.29894212197-0.1709498818390.06054523197360.692443917484-0.1720834717790.8270183180260.023989956620.03680771841450.0555632956448-0.0741815614616-0.119046357519-0.203915393679-0.02958521009130.212831785030.05027917049010.252509196472-0.00209052150844-0.0119479021790.3002029378740.01319057364730.28128403832277.070262918327.275712399335.1770479235
50.279717831453-0.07012851292230.2225102479610.55982351867-0.1384265293330.9893749149620.002147005617820.00674633451886-0.0255857422288-0.04235951939070.0271926579794-0.04028457022320.09093951206720.0191527331219-0.02020838793530.20297029336-0.0174966951219-0.01092197180220.224207980047-0.01438246440930.20841534555474.593009254625.553558312340.641803141
61.517141414130.29067158924-0.7358676010430.299023671914-0.1492547069742.31178255162-0.01864810527940.09441489523490.0145616068815-0.0425627801075-0.001394306884270.02970826800840.0839137212264-0.009088063641050.01777817569530.2384314460790.00200267545839-0.03402307241350.212427878932-0.02175622747390.23604347308270.229831120320.957197759525.7947284961
70.4546617379770.209885987875-0.04340839014140.893133162872-0.3086747082422.01207494398-0.05231887605240.223379115887-0.214497990803-0.04727521601350.0629567148366-0.09997999846860.2892432565620.2547783020970.0558528771940.3362202126440.00966715378253-0.006855704242040.263994747661-0.01788985863750.31616904586577.997608212910.805730738.9330905311
82.39701509712-0.484665149414-0.09905632638421.844256724130.5113026473163.02190092238-0.152954088080.233218692546-0.1525462593610.03420195942790.1277932832710.1858363281830.299296260803-0.128561039096-0.00638820507430.298655311743-0.0220444585346-0.009926084785690.258260801381-0.03648904209420.2705623661972.156834359914.989071333414.6592306605
90.276876155120.2303940030440.004123270420580.559323777017-0.6389433247635.44326665659-0.021300873550.0572384485996-0.134238551879-0.153882256201-0.0553489078567-0.001022504928150.792646045450.1000013620860.06734003267560.3677685292080.05181093699280.003895647983890.274565717539-0.01148834395490.30104865876477.4740689717.6054482018227.242926358
101.335430097640.341111495033-0.4902778579961.45025678787-0.6342977627770.8176421530960.0486313327548-0.0809131979219-0.0649278733886-0.00361500419307-0.0260637379137-0.1643617145920.003582956243170.2238391777550.07614811196050.2324787173370.00277763783252-0.000896351794650.293029381043-0.02834894750720.29093512683498.70925959235.366840232741.2702735036
111.408141889170.29108368325-0.1837464213312.12100780676-0.3231128364341.087789284140.0128105607925-0.335439804051-0.08175926416150.426930647042-0.05304512978980.31617919344-0.0333906277503-0.132406974664-0.01052378756010.311630300383-0.01569884040790.0428697958240.314713584032-0.01934506562290.21007526005966.98262405728.733083896262.9386108279
120.961662351898-0.281770382007-0.3954495830540.2324516938480.1172879288310.3355881090690.012847070340.06883284705080.0691347924185-0.01834927549910.0286238317209-0.06244587386920.0164646065256-0.0303713087758-0.008823969294290.231178554471-0.0205731587118-0.007400096211090.236204221393-0.003748129102880.2260613784380.790777646634.971625100345.413999507
131.23400756783-0.116581303721-0.4174975628480.445784084157-0.1242861059220.7044397954430.04160912065350.04286625514820.26588418338-0.004419246561730.06666211239040.1280023035880.0508952478788-0.129469467053-0.1034017178890.2364220982370.00496729062612-0.01472263708190.217449960404-0.01616393136550.25072292933871.58530333241.571223662941.3691276681
141.403548207550.390673299976-1.009592488790.681928794603-0.7493139322691.041081717660.108388830183-0.2265288037720.02155814113910.0777352415589-0.01885539704080.0290386595052-0.004000034902590.140111697589-0.05320812981450.231713147823-0.0197020253641-0.01069117349220.239288443615-0.0445350844940.21586078658187.164947332241.870129241253.5360700372
151.441982035620.1492574072940.007512555464510.159870816819-0.3339823665620.496078038688-0.0522833838745-0.07597007922770.386406425665-0.02635032244610.05540832451420.0726701935776-0.0687412521466-0.0728376454731-0.08812067001950.281511237754-0.00732844136530.006555256196720.248467702535-0.035403445660.35173743834884.601388615851.25685928440.5526722855
161.42052007040.320799721451-0.1170834014650.565125026430.3610961918251.11902460387-0.09494575035920.1109967395870.26711416713-0.09883872338410.169866127338-0.00183513692002-0.3668765215270.109289559676-0.09648834518740.3076329828390.01226213440310.04983033207150.223464142882-0.02417211813260.29954082337573.422042791153.02323523851.9258263123
171.456553248230.3518090231240.3931584184132.32479096659-0.5461800620822.918963328990.269412710212-0.364393517192-0.1789313789580.459368644651-0.289934116995-0.1064242586210.04659610252730.343201219413-0.0662515764560.274758952648-0.05106294637020.002691378376180.253734574104-0.04903620971560.28360319149297.745626784753.802964585350.4540100093
182.26990677787-1.389467878960.05127386422532.417070399150.2140141795511.332522333320.1163516512750.02952403772770.4218037564310.171516361248-0.0545896340647-0.0811341454822-0.23376290456-0.0625109760511-0.1092292750560.321836799835-0.07683887774710.03334019651740.268712844462-0.07823691812760.46065143968393.961497389963.456397003647.9905203389
190.280786988540.1316249184990.3949725993870.03934348657870.1216589536570.6212793183550.13087007714-0.1346274831130.3487227734410.00707481227834-0.2105140682820.34439072675-0.531392088344-0.1898177882060.08908976800820.3526035792060.03562525768780.02918913360350.236016933211-0.04730836588930.33192718923764.00564697755.43831051252.5181925969
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 22 through 45 )AA22 - 451 - 24
22chain 'A' and (resid 46 through 70 )AA46 - 7025 - 49
33chain 'A' and (resid 71 through 86 )AA71 - 8650 - 65
44chain 'A' and (resid 87 through 125 )AA87 - 12566 - 104
55chain 'A' and (resid 126 through 179 )AA126 - 179105 - 158
66chain 'A' and (resid 180 through 256 )AA180 - 256159 - 235
77chain 'A' and (resid 257 through 288 )AA257 - 288236 - 267
88chain 'A' and (resid 289 through 312 )AA289 - 312268 - 291
99chain 'A' and (resid 313 through 356 )AA313 - 356292 - 325
1010chain 'B' and (resid 23 through 55 )BB23 - 551 - 33
1111chain 'B' and (resid 56 through 86 )BB56 - 8634 - 64
1212chain 'B' and (resid 87 through 152 )BB87 - 15265 - 130
1313chain 'B' and (resid 153 through 179 )BB153 - 179131 - 157
1414chain 'B' and (resid 180 through 241 )BB180 - 241158 - 219
1515chain 'B' and (resid 242 through 272 )BB242 - 272220 - 250
1616chain 'B' and (resid 273 through 288 )BB273 - 288251 - 266
1717chain 'B' and (resid 289 through 312 )BB289 - 312267 - 290
1818chain 'B' and (resid 313 through 338 )BB313 - 338291 - 316
1919chain 'B' and (resid 339 through 356 )BB339 - 356317 - 334

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