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- PDB-5e5n: Ketosynthase from module 6 of the bacillaene synthase from Bacill... -

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Basic information

Entry
Database: PDB / ID: 5e5n
TitleKetosynthase from module 6 of the bacillaene synthase from Bacillus subtilis 168 (C167S mutant, crystal form 1)
ComponentsPolyketide synthase PksL
KeywordsHYDROLASE / trans-AT Ketosynthase / Polyketide
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
Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 - #100 / : / RhiE-like, KS-MAT linker domain / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Prismane-like superfamily / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / : ...Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 - #100 / : / RhiE-like, KS-MAT linker domain / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Prismane-like superfamily / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / Polyketide synthase, dehydratase domain superfamily / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / : / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Beta-ketoacyl synthase / 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 / 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 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Polyketide synthase PksL
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWagner, D.T. / Gay, D.C. / Keatinge-Clay, A.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)26-1606-1550 United States
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
DepositionOct 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_database_related / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_database_related.db_id / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyketide synthase PksL
B: Polyketide synthase PksL
C: Polyketide synthase PksL
D: Polyketide synthase PksL


Theoretical massNumber of molelcules
Total (without water)276,1124
Polymers276,1124
Non-polymers00
Water24,4641358
1
A: Polyketide synthase PksL
C: Polyketide synthase PksL


Theoretical massNumber of molelcules
Total (without water)138,0562
Polymers138,0562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-19 kcal/mol
Surface area42190 Å2
MethodPISA
2
B: Polyketide synthase PksL
D: Polyketide synthase PksL


Theoretical massNumber of molelcules
Total (without water)138,0562
Polymers138,0562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-19 kcal/mol
Surface area42890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.436, 108.194, 151.846
Angle α, β, γ (deg.)90.00, 96.43, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 3 - 591 / Label seq-ID: 25 - 613

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Polyketide synthase PksL / PKS


Mass: 69027.969 Da / Num. of mol.: 4 / Mutation: C192S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: pksL, outG, pksA, pksX, BSU17190 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05470
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1358 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 15 mg/ml protein in 150 mM NaCl and 20 mM HEPES pH 7.5 mixed 1:1 in 1.7 M LiSO4 and 100 mM Tris pH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→150 Å / Num. obs: 183336 / % possible obs: 99.2 % / Redundancy: 2.1 % / Net I/σ(I): 2.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PksKS2 (4NA1)

4na1


Resolution: 2→150 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.914 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23649 9722 5 %RANDOM
Rwork0.2022 ---
obs0.2039 183336 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.025 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→150 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17239 0 0 1358 18597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01917622
X-RAY DIFFRACTIONr_bond_other_d00.0216606
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.96123830
X-RAY DIFFRACTIONr_angle_other_deg3.575338336
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.77152175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47424.484805
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.886153022
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9041586
X-RAY DIFFRACTIONr_chiral_restr0.1050.22579
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02119879
X-RAY DIFFRACTIONr_gen_planes_other0.0280.023935
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_it5.1623.9888763
X-RAY DIFFRACTIONr_mcbond_other5.1613.9888762
X-RAY DIFFRACTIONr_mcangle_it6.5465.94610917
X-RAY DIFFRACTIONr_mcangle_other6.5465.94610918
X-RAY DIFFRACTIONr_scbond_it6.4094.6388859
X-RAY DIFFRACTIONr_scbond_other6.4094.6388860
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.7886.71212914
X-RAY DIFFRACTIONr_long_range_B_refined10.97734.19421411
X-RAY DIFFRACTIONr_long_range_B_other10.96434.09321273
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)
11A684440.11
12B684440.11
21A648620.11
22C648620.11
31A645260.12
32D645260.12
41B648920.11
42C648920.11
51B645020.12
52D645020.12
61C647640.11
62D647640.11
LS refinement shellResolution: 1.997→2.049 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 713 -
Rwork0.25 13049 -
obs--95.98 %

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