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- PDB-7r7g: Synechococcus Olefin Synthase FAAL domain A229I/R336A in complex ... -

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Basic information

Entry
Database: PDB / ID: 7r7g
TitleSynechococcus Olefin Synthase FAAL domain A229I/R336A in complex with palmitoyl adenylate and pyrophosphate
ComponentsPolyketide synthase
KeywordsLIGASE / Fatty acid-AMP ligase (FAAL) Olefin synthase Fatty acid binding protein Polyketide
Function / homology
Function and homology information


Actinobacterium-type cell wall biogenesis / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / nucleotide binding
Similarity search - Function
Disco-interacting protein 2-like, AMP domain / Sulfotransferase family / Fatty acyl-AMP ligase /fatty acyl-CoA ligase / CurL-like, PKS C-terminal / ANL, C-terminal domain / PKS_PP_betabranch / Polyketide synthase, ketoreductase domain / KR domain / ANL, N-terminal domain / : ...Disco-interacting protein 2-like, AMP domain / Sulfotransferase family / Fatty acyl-AMP ligase /fatty acyl-CoA ligase / CurL-like, PKS C-terminal / ANL, C-terminal domain / PKS_PP_betabranch / Polyketide synthase, ketoreductase domain / KR domain / ANL, N-terminal domain / : / AMP-binding enzyme, C-terminal domain / Epoxide hydrolase-like / AMP-binding, conserved site / Putative AMP-binding domain signature. / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / AMP-dependent synthetase/ligase / AMP-binding enzyme / GMP Synthetase; Chain A, domain 3 / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / AMP-binding enzyme, C-terminal domain superfamily / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold / NAD(P)-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
palmitoyl adenylate / ACETATE ION / PYROPHOSPHATE 2- / Polyketide synthase
Similarity search - Component
Biological speciesSynechococcus sp. PCC 7002 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSikkema, A.P. / Strugis, R.M. / Smith, J.L.
Funding support United States, 8items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK042303 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA108874 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118101 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM008270 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)AGM-12006 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)ACB-12002 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM138396 United States
National Institutes of Health/Office of the DirectorOD012289 United States
CitationJournal: To Be Published
Title: An electrostatic fatty acid selection mechanism by the Olefin Synthase FAAL domain from Synechococcus sp. PCC7002
Authors: Sikkema, A.P. / Sturgis, R.M. / Gerwick, W.H. / Sherman, D.H. / Smith, J.L.
History
DepositionJun 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: Polyketide synthase
B: Polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,58610
Polymers123,8962
Non-polymers1,6908
Water5,693316
1
A: Polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7935
Polymers61,9481
Non-polymers8454
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7935
Polymers61,9481
Non-polymers8454
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)201.244, 60.921, 95.752
Angle α, β, γ (deg.)90.000, 101.109, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Polyketide synthase


Mass: 61948.094 Da / Num. of mol.: 2 / Fragment: FAAL domain / Mutation: A229I, R336A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. PCC 7002 (bacteria) / Strain: ATCC 27264 / PCC 7002 / PR-6 / Gene: SYNPCC7002_A1173 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B1XKC6, long-chain-fatty-acid-[acyl-carrier-protein] ligase

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Non-polymers , 5 types, 324 molecules

#2: Chemical ChemComp-1TF / palmitoyl adenylate / 5'-O-[(R)-(hexadecanoyloxy)(hydroxy)phosphoryl]adenosine


Mass: 585.630 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H44N5O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.24 Å3/Da / Density % sol: 45.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.17-0.21 M NDSB-256 (Dimethylbenzylammonium Propane Sulfonate), 26-33% PEG 3350, 0.19-0.21 M ammonium acetate, 0.1M sodium acetate pH 5.5).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 12, 2016
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.25→29.41 Å / Num. obs: 103053 / % possible obs: 99.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 36.8 Å2 / CC1/2: 0.99 / CC star: 0.997 / Rmerge(I) obs: 0.144 / Net I/σ(I): 6.6
Reflection shellResolution: 2.25→2.38 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.663 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 17036 / CC1/2: 0.896 / CC star: 0.972 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LNV

3lnv


Resolution: 2.25→29.41 Å / SU ML: 0.3731 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.652
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2557 3779 3.67 %
Rwork0.2295 99089 -
obs0.2304 102868 96.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.53 Å2
Refinement stepCycle: LAST / Resolution: 2.25→29.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8587 0 108 316 9011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01248873
X-RAY DIFFRACTIONf_angle_d1.641212066
X-RAY DIFFRACTIONf_chiral_restr0.1041354
X-RAY DIFFRACTIONf_plane_restr0.00581575
X-RAY DIFFRACTIONf_dihedral_angle_d18.56833170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.270.46131300.3733336X-RAY DIFFRACTION87.06
2.27-2.30.37021360.35043568X-RAY DIFFRACTION95.74
2.3-2.340.40351480.34753768X-RAY DIFFRACTION96.38
2.34-2.370.41611340.33253571X-RAY DIFFRACTION96.38
2.37-2.40.34521320.32663612X-RAY DIFFRACTION96.07
2.4-2.440.34121460.32483708X-RAY DIFFRACTION96.4
2.44-2.480.33981340.32233591X-RAY DIFFRACTION95.86
2.48-2.520.37921380.32363709X-RAY DIFFRACTION95.77
2.53-2.570.34541420.31783666X-RAY DIFFRACTION95.68
2.57-2.620.37491360.31053628X-RAY DIFFRACTION96.41
2.62-2.670.3551410.2883642X-RAY DIFFRACTION96.43
2.67-2.730.28951400.28453561X-RAY DIFFRACTION94.95
2.73-2.80.34441370.28913657X-RAY DIFFRACTION96.29
2.8-2.870.27651480.28453767X-RAY DIFFRACTION97.75
2.87-2.940.29541390.28753720X-RAY DIFFRACTION97.94
2.94-3.030.30091420.27523699X-RAY DIFFRACTION97.76
3.03-3.130.34661420.26273676X-RAY DIFFRACTION97.67
3.13-3.240.23241480.23763743X-RAY DIFFRACTION97.99
3.24-3.370.23361450.21613712X-RAY DIFFRACTION97.82
3.37-3.520.18991410.20463729X-RAY DIFFRACTION97.26
3.52-3.710.25381310.20023594X-RAY DIFFRACTION96.1
3.71-3.940.21931430.17293704X-RAY DIFFRACTION97.32
3.94-4.240.1961390.17663685X-RAY DIFFRACTION97.33
4.24-4.670.20141390.16043812X-RAY DIFFRACTION99.12
4.67-5.340.16861470.17293756X-RAY DIFFRACTION99.21
5.34-6.710.22221420.18863748X-RAY DIFFRACTION98.26
6.71-29.410.15131390.16043727X-RAY DIFFRACTION98.65
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)
11.059359572390.3675198883490.06768252910141.522987803010.3917984951241.57490421492-0.00136692412880.0856174900678-0.0361492902566-0.02717254301060.008116162716480.07435305499160.0112807400863-0.0505795285931-0.001562919029790.4736692392160.006912554947590.001080949328740.161363133837-0.002983600000050.269985005899-21.359891219415.51077307859.67547863968
21.267720750390.0298178175735-0.0868042078751.298796995760.1802811785510.5221996253770.0138438826422-0.1087875736290.1545869359790.235933322249-0.02201394629390.0569404530082-0.137298836006-0.06559871815110.01000516000110.5083488118090.02916053916860.008814423318990.195951225772-0.004448495678430.231213771927-29.171188339732.038055241525.6139144465
34.90090786561-1.679626865111.214568728110.964690616769-0.9989354823741.20703168658-0.22552283574-0.08436221299360.331731554369-0.08965448520370.1121807046050.018128743693-0.247300050835-0.2302878996950.05538946913260.5755418266250.0202344325330.003911258745420.216661450831-0.04437051280690.364564244098-32.043634932546.155787774721.037157073
44.43034489691-1.7129395932-0.1061858132880.7818331159360.05997666290291.55853887412-0.0337677112278-0.0132027519732-0.317824891388-0.1087726649260.04151584143250.02464891020940.0517986614007-0.0787815028095-0.04257870340360.4518016267090.00597168332968-0.008760688980480.2310475424240.003372740020760.310104513774-45.984591969244.6472804329.3052498837
51.91505050905-0.147738353140.1885833184262.931616600330.09246130729411.18300058675-0.0556165364740.01032326133090.169201758570.146379168060.00647489399475-0.0108771954633-0.1830793811490.06361537314380.008055938563340.485355489232-0.022436193502-0.0005944863001550.1647426667270.01730867518380.24920915872515.309597618156.648153790118.5830487973
63.093571970510.14695486471-0.6989377020133.10412477161-0.002611859919891.202630858590.04654488834660.205303249005-0.0789694072387-0.0569618632892-0.0695727599802-0.2973874906460.01049315523940.05571042744750.03202081947030.482882045878-0.00729627052633-0.03666843057730.2165999717830.006325408665110.22356272402619.493499997850.12596493148.14968144415
71.177226932750.1486621332270.3558225552090.742421033802-0.2765010274891.15859604010.0788289498727-0.138553352988-0.05101474135930.371188082684-0.06696106333320.0648675368916-0.0002549557581190.0688896782951-0.01196050210790.636291176502-0.01165469057710.01394002806460.1920088033890.002318402447880.28407900038315.7864982438.052748456433.4491413286
83.24086876944-1.31283729767-0.1903639552961.0136828240.6262019853350.914814981838-0.155956849282-0.0863843443956-0.5403554612370.3838971242710.1289615710580.2141762926080.407470792710.2240303588530.04357177714580.7577235662160.0284603694433-0.0420878809040.2228135469730.04265420479660.39393981655621.650714181921.941553424131.8296844461
94.184384789220.03472067221170.2269134215453.244260532060.08984590287932.69891060359-0.0168254750078-0.3601180974380.003866462949520.1374791126160.0126020402766-0.2290762740990.4432111309320.3124614432150.01910987633820.5366342612460.116014648085-0.05360654970920.3392169572660.04443321315890.30813437116139.741674687821.316867641929.5351880225
103.666517636650.542358760329-0.3939094456191.063937500580.1018345365862.5652338693-0.0169216352867-0.0574608555611-0.04636143063330.05086415090850.0730649911881-0.1136277009620.07512433874320.294051045648-0.02746284888440.5840794243480.0732327616741-0.04090640662080.314493650552-0.01147304527650.29895576772437.000706492524.881652553521.7675198893
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 227 )AA2 - 2271 - 226
22chain 'A' and (resid 228 through 434 )AA228 - 434227 - 431
33chain 'A' and (resid 435 through 471 )AA435 - 471432 - 468
44chain 'A' and (resid 472 through 570 )AA472 - 570469 - 567
55chain 'B' and (resid 2 through 100 )BC2 - 1001 - 99
66chain 'B' and (resid 101 through 177 )BC101 - 177100 - 176
77chain 'B' and (resid 178 through 434 )BC178 - 434177 - 431
88chain 'B' and (resid 435 through 472 )BC435 - 472432 - 469
99chain 'B' and (resid 473 through 526 )BC473 - 526470 - 523
1010chain 'B' and (resid 527 through 570 )BC527 - 570524 - 567

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