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- PDB-7r7f: Synechococcus Olefin Synthase FAAL domain R336A in complex with s... -

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Basic information

Entry
Database: PDB / ID: 7r7f
TitleSynechococcus Olefin Synthase FAAL domain R336A in complex with stearoyl 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
stearoyl adenylate / ACETATE ION / PYROPHOSPHATE 2- / Polyketide synthase
Similarity search - Component
Biological speciesSynechococcus sp. PCC 7002 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 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)125,55810
Polymers123,8122
Non-polymers1,7468
Water7,008389
1
A: Polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7795
Polymers61,9061
Non-polymers8734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7795
Polymers61,9061
Non-polymers8734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)199.087, 60.602, 95.143
Angle α, β, γ (deg.)90.000, 101.111, 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: 61906.016 Da / Num. of mol.: 2 / Fragment: FAAL domain / Mutation: 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, 397 molecules

#2: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-1T1 / stearoyl adenylate / 5'-O-[(R)-hydroxy(octadecanoyloxy)phosphoryl]adenosine


Mass: 613.683 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H48N5O8P / 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.: 389 / 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: 2.19 Å3/Da / Density % sol: 43.8 %
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: Apr 21, 2016
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.13→50.5 Å / Num. obs: 119685 / % possible obs: 99.2 % / Redundancy: 4.1 % / Biso Wilson estimate: 30.23 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.126 / Net I/σ(I): 8.2
Reflection shellResolution: 2.13→2.26 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.753 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 19634 / CC1/2: 0.684 / CC star: 0.901 / % possible all: 97.1

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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: 2.13→50.5 Å / SU ML: 0.3292 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.2405
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2453 3816 3.19 %
Rwork0.2107 115847 -
obs0.2118 119663 97.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.4 Å2
Refinement stepCycle: LAST / Resolution: 2.13→50.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8638 0 112 389 9139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00898928
X-RAY DIFFRACTIONf_angle_d1.135612129
X-RAY DIFFRACTIONf_chiral_restr0.06641352
X-RAY DIFFRACTIONf_plane_restr0.00721585
X-RAY DIFFRACTIONf_dihedral_angle_d17.94733217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.150.34511190.33843638X-RAY DIFFRACTION83.64
2.15-2.180.34371420.32634288X-RAY DIFFRACTION97.77
2.18-2.210.34311370.3364356X-RAY DIFFRACTION96.89
2.21-2.240.3791420.32424242X-RAY DIFFRACTION97.23
2.24-2.280.33121380.32494255X-RAY DIFFRACTION97.93
2.28-2.310.33331440.30334320X-RAY DIFFRACTION97.87
2.31-2.350.33131400.29334288X-RAY DIFFRACTION98.16
2.35-2.390.34721470.28484307X-RAY DIFFRACTION97.91
2.39-2.430.29191420.27484364X-RAY DIFFRACTION98.06
2.43-2.480.31781450.25814287X-RAY DIFFRACTION98.1
2.48-2.530.33181340.24824273X-RAY DIFFRACTION97.11
2.53-2.590.26881480.26244294X-RAY DIFFRACTION98.58
2.59-2.650.28671420.25584356X-RAY DIFFRACTION98.45
2.65-2.710.3331420.24784265X-RAY DIFFRACTION97.65
2.71-2.790.32611450.24024357X-RAY DIFFRACTION98.64
2.79-2.870.25091430.22684301X-RAY DIFFRACTION98.45
2.87-2.960.21841440.2254379X-RAY DIFFRACTION98.97
2.96-3.070.2311390.21434366X-RAY DIFFRACTION98.69
3.07-3.190.28991450.20914298X-RAY DIFFRACTION98.36
3.19-3.340.25791440.19494313X-RAY DIFFRACTION98.48
3.34-3.510.25021380.18474304X-RAY DIFFRACTION98.51
3.51-3.730.21241400.17514335X-RAY DIFFRACTION98.27
3.73-4.020.19311440.1614361X-RAY DIFFRACTION98.47
4.02-4.420.18651420.16124299X-RAY DIFFRACTION98.86
4.42-5.060.17331430.1584323X-RAY DIFFRACTION98.15
5.06-6.380.19661420.17284338X-RAY DIFFRACTION98.53
6.38-50.50.15871450.15334340X-RAY DIFFRACTION98.75
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)
10.7407344049770.178885534101-0.144967348972.03548774468-0.969751535242.953153082370.02821568224060.101443073346-0.0650970291732-0.02413978604830.08532964908510.2269284665690.028329423611-0.132935169298-0.1075376957320.175730783250.005180180356940.001904889717560.147490864426-0.04205578282260.218293380197-22.566378307513.48895283446.95575647976
20.9101981502650.148959183476-0.006372557858631.02267070122-0.1040479351720.6836771391990.0182737139736-0.05360671007380.05514990029410.129706705757-0.01570390732920.131586605657-0.0588778983179-0.09903708992560.000345829059560.2311402664510.007719950002140.01309885600290.205800230045-0.0172881093320.222813791601-25.898301550127.78707637621.6856483907
33.56432110918-1.50428045892.147359108890.775260717283-1.058801794551.84692459983-0.0734872885837-0.06422817317710.03956450109250.04438800070110.04324495899780.0395992790014-0.0380688418106-0.1469125147450.05574735707860.2723956701080.009063499864320.01569832869720.227455612086-0.0227878898870.306665055555-32.434276535845.894138257720.9622016873
44.55393345557-0.815102527285-0.1151439795842.267388183630.6215476088442.92449210135-0.0291715542658-0.108845958651-0.298181902883-0.138551792759-0.03961288587340.1665759485310.085270899997-0.2026536231420.04860804732630.1693143635990.0152198687595-0.002388233989560.250455715285-0.003668592950260.329680276424-45.463594179544.61092413629.03289678714
51.84784876243-0.04454669771240.3605630594462.536450300080.8149922582593.455884581980.02168554824610.1026557548660.138807365860.160810706274-0.00836196996845-0.0720532923109-0.132113607470.111619675399-0.01050709788330.266866722984-0.01978242178780.0243650672580.1481202877970.03528686491120.19541743504215.340907815156.452848918618.506827214
62.067335831460.345063663324-0.7466518262714.22397553903-0.642295406371.09660426672-0.08882376567140.208073939463-0.0650578025035-0.246132658788-0.01462921426-0.4281197954650.09403203997410.125441651480.1103777180880.238195423353-0.0141045276798-0.04302521449230.284859073712-0.006616256175950.15473507431919.441656152749.90158818438.17143663434
70.932192833898-0.03239648726190.3721383887481.435835162020.116920676751.111786828680.0301045676177-0.128786436262-0.0712278982120.2755780039390.00145394001845-0.00214003471228-0.009511640565560.125937232767-0.03367605651490.266016316329-0.006715126193180.003764297791350.2200775890480.01895779154690.16524264977415.905571892637.961588996733.3165686149
85.30384279358-1.75263869213-0.9963652108792.392317651180.1515042918042.2395888062-0.0752707452952-0.184089577254-0.1840024446460.3595748150690.127444709008-0.07634657192280.1452215060940.33415117869-0.06911119867480.326872117580.018122501722-0.06265459666890.2130158432470.008054045765710.20636001066521.986963767322.052198432631.7919074931
94.930503109520.2229884078540.239329620232.99007852571-1.649171767464.870499850910.0528990257344-0.3514119376870.1888639594180.1966452570140.0602134660339-0.3854793585150.1293962753420.471921851662-0.1026983939590.2484942440130.0779649849404-0.04545182001520.324328891867-0.04066049070850.28932249285338.279212562323.065109654725.662940734
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 133 )AA2 - 1331 - 132
22chain 'A' and (resid 134 through 434 )AA134 - 434133 - 431
33chain 'A' and (resid 435 through 473 )AA435 - 473432 - 470
44chain 'A' and (resid 474 through 570 )AA474 - 570471 - 567
55chain 'B' and (resid 2 through 100 )BB2 - 1001 - 99
66chain 'B' and (resid 101 through 177 )BB101 - 177100 - 176
77chain 'B' and (resid 178 through 434 )BB178 - 434177 - 431
88chain 'B' and (resid 435 through 473 )BB435 - 473432 - 470
99chain 'B' and (resid 474 through 570 )BB474 - 570471 - 567

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