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- PDB-5eny: Ketosynthase from module 6 connected to acyl carrier protein from... -

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Basic information

Entry
Database: PDB / ID: 5eny
TitleKetosynthase from module 6 connected to acyl carrier protein from module 5 (unobservable) of the bacillaene synthase from Bacillus subtilis 168
ComponentsPolyketide synthase PksL
KeywordsHYDROLASE / trans-AT ketosynthase / polyketide / bacillaene
Function / homology
Function and homology information


DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process / oxidoreductase activity / cytoplasm
Similarity search - Function
Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / : / Prismane-like superfamily / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily ...Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / : / Prismane-like superfamily / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / PKS_KR / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / 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 / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyketide synthase PksL
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 4 Å
AuthorsWagner, D.T. / Gay, D.C. / Keatinge-Clay, A.T.
CitationJournal: J.Struct.Biol. / Year: 2016
Title: The LINKS motif zippers trans-acyltransferase polyketide synthase assembly lines into a biosynthetic megacomplex.
Authors: Gay, D.C. / Wagner, D.T. / Meinke, J.L. / Zogzas, C.E. / Gay, G.R. / Keatinge-Clay, A.T.
History
DepositionNov 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyketide synthase PksL
B: Polyketide synthase PksL
C: Polyketide synthase PksL
D: Polyketide synthase PksL
E: Polyketide synthase PksL
F: Polyketide synthase PksL
G: Polyketide synthase PksL
H: Polyketide synthase PksL


Theoretical massNumber of molelcules
Total (without water)686,5608
Polymers686,5608
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17380 Å2
ΔGint-83 kcal/mol
Surface area165580 Å2
2
A: Polyketide synthase PksL
B: Polyketide synthase PksL


Theoretical massNumber of molelcules
Total (without water)171,6402
Polymers171,6402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-19 kcal/mol
Surface area42210 Å2
MethodPISA
3
C: Polyketide synthase PksL
D: Polyketide synthase PksL


Theoretical massNumber of molelcules
Total (without water)171,6402
Polymers171,6402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-19 kcal/mol
Surface area42050 Å2
MethodPISA
4
E: Polyketide synthase PksL
F: Polyketide synthase PksL


Theoretical massNumber of molelcules
Total (without water)171,6402
Polymers171,6402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-19 kcal/mol
Surface area42100 Å2
MethodPISA
5
G: Polyketide synthase PksL
H: Polyketide synthase PksL


Theoretical massNumber of molelcules
Total (without water)171,6402
Polymers171,6402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-19 kcal/mol
Surface area42090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.106, 112.732, 211.441
Angle α, β, γ (deg.)104.96, 90.07, 106.32
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A3 - 591
2010B3 - 591
1020A3 - 591
2020C3 - 591
1030A3 - 591
2030D3 - 591
1040A3 - 591
2040E3 - 591
1050A3 - 591
2050F3 - 591
1060A3 - 591
2060G3 - 591
1070A3 - 591
2070H3 - 591
1080B3 - 591
2080C3 - 591
1090B3 - 591
2090D3 - 591
10100B3 - 591
20100E3 - 591
10110B3 - 591
20110F3 - 591
10120B3 - 591
20120G3 - 591
10130B3 - 591
20130H3 - 591
10140C3 - 591
20140D3 - 591
10150C3 - 591
20150E3 - 591
10160C3 - 591
20160F3 - 591
10170C3 - 591
20170G3 - 591
10180C3 - 591
20180H3 - 591
10190D3 - 591
20190E3 - 591
10200D3 - 591
20200F3 - 591
10210D3 - 591
20210G3 - 591
10220D3 - 591
20220H3 - 591
10230E3 - 591
20230F3 - 591
10240E3 - 591
20240G3 - 591
10250E3 - 591
20250H3 - 591
10260F3 - 591
20260G3 - 591
10270F3 - 591
20270H3 - 591
10280G3 - 591
20280H3 - 591

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

#1: Protein
Polyketide synthase PksL / PKS


Mass: 85819.969 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: pksL, outG, pksA, pksX, BSU17190 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05470

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 25 mg/ml PksACP5+KS6, 150 mM NaCl, 10% glycerol, 10 mM HEPES, pH 7.5) with 1 uL crystallization buffer (30% PEG 4000 (v/v), 0.2 M sodium acetate, 0.1 M Tris, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4→39.77 Å / Num. obs: 23712 / % possible obs: 98.7 % / Redundancy: 3.3 % / Net I/σ(I): 6.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 4→39.77 Å / Cor.coef. Fo:Fc: 0.822 / Cor.coef. Fo:Fc free: 0.797 / Cross valid method: THROUGHOUT / ESU R Free: 1.375 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.354 2126 5.1 %RANDOM
Rwork0.33349 ---
obs0.33451 -92.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 154.659 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.03 Å20.02 Å2
2---0.18 Å2-0.05 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 4→39.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34416 0 0 0 34416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01935180
X-RAY DIFFRACTIONr_bond_other_d00.0233136
X-RAY DIFFRACTIONr_angle_refined_deg0.8521.96147576
X-RAY DIFFRACTIONr_angle_other_deg3.58376484
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.97554340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72724.4911612
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.181156020
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.26715172
X-RAY DIFFRACTIONr_chiral_restr0.0680.25148
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02139700
X-RAY DIFFRACTIONr_gen_planes_other0.0050.027864
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it8.16315.38217492
X-RAY DIFFRACTIONr_mcbond_other8.16315.38217491
X-RAY DIFFRACTIONr_mcangle_it12.0323.04521788
X-RAY DIFFRACTIONr_mcangle_other12.0323.04621789
X-RAY DIFFRACTIONr_scbond_it7.47615.85617688
X-RAY DIFFRACTIONr_scbond_other7.47615.85617689
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.01123.61725789
X-RAY DIFFRACTIONr_long_range_B_refined17.9338919
X-RAY DIFFRACTIONr_long_range_B_other17.92938920
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A629860.15
12B629860.15
21A702780.12
22C702780.12
31A630360.16
32D630360.16
41A700220.13
42E700220.13
51A630780.16
52F630780.16
61A700000.12
62G700000.12
71A642860.12
72H642860.12
81B630920.15
82C630920.15
91B659980.11
92D659980.11
101B634100.15
102E634100.15
111B655580.12
112F655580.12
121B640700.12
122G640700.12
131B654360.13
132H654360.13
141C633540.15
142D633540.15
151C703160.12
152E703160.12
161C640620.13
162F640620.13
171C701260.12
172G701260.12
181C632560.15
182H632560.15
191D642420.12
192E642420.12
201D660520.12
202F660520.12
211D634660.15
212G634660.15
221D656460.13
222H656460.13
231E633040.15
232F633040.15
241E708900.1
242G708900.1
251E633060.16
252H633060.16
261F630340.15
262G630340.15
271F656020.12
272H656020.12
281G632760.16
282H632760.16
LS refinement shellResolution: 4.004→4.107 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 129 -
Rwork0.383 2247 -
obs--71.54 %

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