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- PDB-7r7e: Synechococcus Olefin Synthase FAAL domain in complex with AMP and... -

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Basic information

Entry
Database: PDB / ID: 7r7e
TitleSynechococcus Olefin Synthase FAAL domain in complex with AMP and pyrophosphate
ComponentsPolyketide synthase
KeywordsLIGASE / Fatty acid-AMP ligase (FAAL) Olefin synthase Fatty acid binding protein Polyketide
Function / homology
Function and homology information


: / DIM/DIP cell wall layer assembly / fatty acid synthase activity / secondary metabolite biosynthetic process / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / nucleotide binding / plasma membrane / cytoplasm
Similarity search - Function
Sulfotransferase family / Fatty acyl-AMP ligase /fatty acyl-CoA ligase / PKS_PP_betabranch / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / ANL, N-terminal domain / PKS_KR / Acyl transferase domain superfamily ...Sulfotransferase family / Fatty acyl-AMP ligase /fatty acyl-CoA ligase / PKS_PP_betabranch / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / ANL, N-terminal domain / PKS_KR / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / AMP-binding, conserved site / Putative AMP-binding domain signature. / Epoxide hydrolase-like / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / 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
Similarity search - Domain/homology
ACETATE ION / ADENOSINE MONOPHOSPHATE / PYROPHOSPHATE 2- / Polyketide synthase
Similarity search - Component
Biological speciesSynechococcus sp. PCC 7002 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsSikkema, A.P. / Strugis, R.M. / Smith, J.L.
Funding support United States, 7items
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
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)125,19710
Polymers123,9842
Non-polymers1,2138
Water11,854658
1
A: Polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5995
Polymers61,9921
Non-polymers6074
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5995
Polymers61,9921
Non-polymers6074
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)201.288, 60.920, 95.929
Angle α, β, γ (deg.)90.000, 101.175, 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: 61992.133 Da / Num. of mol.: 2 / Fragment: FAAL domain
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, 666 molecules

#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 658 / 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: 45.2 %
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-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 10, 2015
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.99→29.82 Å / Num. obs: 140435 / % possible obs: 97 % / Redundancy: 3.1 % / Biso Wilson estimate: 28.25 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.094 / Net I/σ(I): 9
Reflection shellResolution: 1.99→2.11 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.647 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 20450 / CC1/2: 0.708 / CC star: 0.991 / % possible all: 86.9

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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: 1.99→29.82 Å / SU ML: 0.2939 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.049
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2391 3625 2.58 %
Rwork0.1964 136752 -
obs0.1975 140377 92.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.49 Å2
Refinement stepCycle: LAST / Resolution: 1.99→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8652 0 74 658 9384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01238904
X-RAY DIFFRACTIONf_angle_d1.16712105
X-RAY DIFFRACTIONf_chiral_restr0.06981352
X-RAY DIFFRACTIONf_plane_restr0.00821585
X-RAY DIFFRACTIONf_dihedral_angle_d16.72093211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.020.3262840.35032973X-RAY DIFFRACTION52.79
2.02-2.050.34861080.3253979X-RAY DIFFRACTION69.68
2.05-2.080.34041210.32364409X-RAY DIFFRACTION76.91
2.08-2.110.37431370.31745026X-RAY DIFFRACTION87.4
2.11-2.140.32871390.30125409X-RAY DIFFRACTION94.58
2.14-2.180.32521520.27685613X-RAY DIFFRACTION98.19
2.18-2.210.29431430.26725601X-RAY DIFFRACTION97.95
2.21-2.250.35871370.3065295X-RAY DIFFRACTION92.82
2.25-2.30.33681410.28495387X-RAY DIFFRACTION94.98
2.3-2.340.31321440.25155589X-RAY DIFFRACTION95.85
2.34-2.390.32571340.24645167X-RAY DIFFRACTION91.67
2.39-2.450.26531450.23885407X-RAY DIFFRACTION94.29
2.45-2.510.26071430.2165337X-RAY DIFFRACTION94.08
2.51-2.580.26471470.2195689X-RAY DIFFRACTION98.97
2.58-2.660.2921450.21725600X-RAY DIFFRACTION98.21
2.66-2.740.25971480.21425493X-RAY DIFFRACTION96.61
2.74-2.840.23941500.20465552X-RAY DIFFRACTION96.55
2.84-2.950.22661410.21225306X-RAY DIFFRACTION93.3
2.95-3.090.26021470.20045387X-RAY DIFFRACTION93.81
3.09-3.250.22141510.18285585X-RAY DIFFRACTION98.68
3.25-3.450.21391460.17115599X-RAY DIFFRACTION97.79
3.45-3.720.22281410.16325400X-RAY DIFFRACTION94.62
3.72-4.090.20471440.14635283X-RAY DIFFRACTION92.26
4.09-4.680.18211520.13675670X-RAY DIFFRACTION98.73
4.68-5.890.16861400.14935449X-RAY DIFFRACTION95.57
5.89-29.820.18481450.15455547X-RAY DIFFRACTION97.13
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)
11.204312262740.118057339924-0.06136412486092.60716379169-0.5546685654931.7431702193-0.008350700456750.166243296748-0.075365948669-0.1299177241570.05799162022220.1894734393530.0762155725924-0.137194449912-0.03718964179270.158880515816-0.007092946124920.01535073178630.171434210296-0.03264903229070.158538386183-21.349978505912.38344334566.32543882222
21.511627521030.00964459317788-0.08835057409761.538096300350.269525155790.592173936629-0.0414460482432-0.1098679160140.1371839142870.2118810517538.42676041225E-50.194188604649-0.0135384947804-0.1221820895530.02806913283710.2288509481210.01182217250720.01749266832560.197001877444-0.02355206079290.161070749535-28.219598715130.240704123924.4209721625
35.15773536257-0.957229744688-0.3461531606862.164625180921.078071673664.08588934413-0.00838510615846-0.0601056568039-0.398779486418-0.0671710403832-0.08221710660450.1453482654410.0385935653837-0.2093768980120.06911161852260.1682598128290.00444328777280.0008257870348120.2412841910140.0180318693340.294010228663-46.013401946942.88876313789.37325610279
41.586978456030.218386564941-0.03672410284633.097993095890.2275270326471.766282787240.03593511414390.1289770494380.0631381803981-0.0255401901873-0.00234086370239-0.228809358739-0.08389890887750.183478065153-0.03459997926050.171786161527-0.01832254904310.001130719549640.1679961615620.02405013144890.13475377844217.234967513951.949708434614.0087844088
51.197759179960.1370730442330.5269235657791.32180388238-0.1602897086171.229472380090.0299382242337-0.13545949436-0.06365760567920.324843798935-0.04912380943570.00681746591716-0.02295105833460.09796644953250.03033067192060.288382892406-0.007427933841110.02888369188740.2036125533830.01771264358920.16241118008915.920718353336.216071045733.5873100158
66.76503198117-2.65997611553-0.0908393662172.68064855140.02674523025222.54895419262-0.184930551718-0.08237580406-0.6005810497070.3179234841440.1270469716360.01245052519550.2919463719450.276223450550.0669554533830.3206298032570.0043820568902-0.03464486577450.1726362309070.02208315011040.28520195984522.173562712319.897097139632.0448641046
74.97903651431-0.3267103260341.042672583143.68517675629-1.06363967854.65287114138-0.0921264621413-0.2111942663270.02039715342140.2186848241540.0805466040213-0.2777417315960.2637239829670.2790983802250.004110764178130.2272388927550.0670830077633-0.03550441901510.280573053981-0.01819576559470.20516058244238.473889629820.994325425925.8559634149
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 177 )AA2 - 1771 - 176
22chain 'A' and (resid 178 through 471 )AA178 - 471177 - 468
33chain 'A' and (resid 472 through 570 )AA472 - 570469 - 567
44chain 'B' and (resid 2 through 177 )BC2 - 1771 - 176
55chain 'B' and (resid 178 through 434 )BC178 - 434177 - 431
66chain 'B' and (resid 435 through 473 )BC435 - 473432 - 470
77chain 'B' and (resid 474 through 570 )BC474 - 570471 - 567

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