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- PDB-8qk4: Dehydratase domain (PksJ DH1) from the bacillaene trans-AT PKS -

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Basic information

Entry
Database: PDB / ID: 8qk4
TitleDehydratase domain (PksJ DH1) from the bacillaene trans-AT PKS
ComponentsPolyketide synthase PksJ
KeywordsLYASE / dehydratase domain / trans-AT polyketide synthase
Function / homology
Function and homology information


DIM/DIP cell wall layer assembly / fatty acid synthase activity / ligase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process / cytoplasm
Similarity search - Function
RhiE-like, KS-MAT linker domain / : / Polyketide synthase dehydratase N-terminal domain / Condensation domain / Condensation domain / Amino acid adenylation domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain ...RhiE-like, KS-MAT linker domain / : / Polyketide synthase dehydratase N-terminal domain / Condensation domain / Condensation domain / Amino acid adenylation domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / Polyketide synthase, dehydratase domain superfamily / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / PKS_PP_betabranch / Polyketide synthase, ketoreductase domain / KR domain / : / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / PKS_KR / 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 / AMP-binding enzyme, C-terminal domain superfamily / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Polyketide synthase PksJ
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPang, F. / Alkhalaf, L.M. / Jenner, M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R012121/1 United Kingdom
UK Research and Innovation (UKRI)MR/W011247/1 United Kingdom
CitationJournal: To Be Published
Title: Dehydratase domain (PksJ DH1) from the bacillaene trans-AT PKS
Authors: Pang, F. / Alkhalaf, L.M. / Jenner, M.
History
DepositionSep 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyketide synthase PksJ
B: Polyketide synthase PksJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,72710
Polymers74,1852
Non-polymers5428
Water3,423190
1
A: Polyketide synthase PksJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6349
Polymers37,0921
Non-polymers5428
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polyketide synthase PksJ


Theoretical massNumber of molelcules
Total (without water)37,0921
Polymers37,0921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.905, 84.790, 131.938
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Polyketide synthase PksJ / PKS


Mass: 37092.449 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: pksJ, pksK, BSU17180 / Production host: Escherichia coli (E. coli) / References: UniProt: P40806
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.99 Å3/Da / Density % sol: 38.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 22% PEG 3350 and 0.3 M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→49.104 Å / Num. obs: 47606 / % possible obs: 99.95 % / Redundancy: 13.3 % / Biso Wilson estimate: 27.8 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.09
Reflection shellResolution: 1.9→1.97 Å / Num. unique obs: 4715 / CC1/2: 0.975

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→49.104 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.204 / WRfactor Rwork: 0.162 / SU B: 3.916 / SU ML: 0.109 / Average fsc free: 0.9645 / Average fsc work: 0.9726 / Cross valid method: FREE R-VALUE / ESU R: 0.141 / ESU R Free: 0.133
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2163 2247 4.72 %
Rwork0.1761 45359 -
all0.178 --
obs-47606 99.977 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 32.718 Å2
Baniso -1Baniso -2Baniso -3
1-1.916 Å2-0 Å20 Å2
2---1.625 Å2-0 Å2
3----0.291 Å2
Refinement stepCycle: LAST / Resolution: 1.9→49.104 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4315 0 33 190 4538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124500
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164213
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.6386106
X-RAY DIFFRACTIONr_angle_other_deg0.4681.5699709
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0215584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.368522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.72110733
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.97310199
X-RAY DIFFRACTIONr_chiral_restr0.0650.2704
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025297
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02991
X-RAY DIFFRACTIONr_nbd_refined0.2040.2716
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.23818
X-RAY DIFFRACTIONr_nbtor_refined0.1730.22133
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.22451
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2213
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2370.229
X-RAY DIFFRACTIONr_nbd_other0.2550.2102
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2070.224
X-RAY DIFFRACTIONr_mcbond_it3.2363.2542306
X-RAY DIFFRACTIONr_mcbond_other3.2373.2542306
X-RAY DIFFRACTIONr_mcangle_it4.8815.8192882
X-RAY DIFFRACTIONr_mcangle_other4.885.8192883
X-RAY DIFFRACTIONr_scbond_it4.113.6632194
X-RAY DIFFRACTIONr_scbond_other4.1093.6642195
X-RAY DIFFRACTIONr_scangle_it6.5426.493218
X-RAY DIFFRACTIONr_scangle_other6.5416.493219
X-RAY DIFFRACTIONr_lrange_it8.62636.9324680
X-RAY DIFFRACTIONr_lrange_other8.59436.3854638
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.9-1.9490.2851570.30533170.30434780.9130.91699.8850.296
1.949-2.0030.2751620.24431910.24533540.9490.95499.97020.228
2.003-2.0610.2431470.22331430.22432900.9590.9631000.201
2.061-2.1240.2311550.230850.20232400.9640.971000.177
2.124-2.1930.2271400.19329340.19430740.9690.9741000.168
2.193-2.270.2081360.18128570.18329930.970.9781000.155
2.27-2.3560.2011360.16827610.16928980.9740.98299.96550.144
2.356-2.4520.2261200.17726920.17928120.9710.981000.147
2.452-2.560.2251270.16925660.17226930.9710.9821000.143
2.56-2.6850.2181340.1724320.17225660.9720.9811000.144
2.685-2.830.2241250.16923320.17224570.970.9831000.146
2.83-3.0010.1831120.16522130.16623250.9760.9831000.143
3.001-3.2070.2071170.17520760.17721930.9710.9811000.158
3.207-3.4630.232930.17619660.17820590.970.9811000.159
3.463-3.7910.235880.17218100.17518980.9680.9831000.163
3.791-4.2360.181700.14416640.14617340.9810.9871000.14
4.236-4.8850.147780.12914600.1315380.9890.9911000.134
4.885-5.9680.239730.17312470.17713200.9680.9861000.176
5.968-8.3790.232490.19710000.19810490.9660.981000.202
8.379-49.1040.292280.1966130.26430.9330.97499.6890.23

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