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

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Basic information

Entry
Database: PDB / ID: 5erf
TitleKetosynthase from module 6 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 / Thiolase-like / Phosphopantetheine attachment site. / 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: 3.1 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) 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
DepositionNov 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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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


Theoretical massNumber of molelcules
Total (without water)138,0882
Polymers138,0882
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-17 kcal/mol
Surface area42470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.057, 77.317, 85.291
Angle α, β, γ (deg.)77.91, 70.26, 64.18
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A3 - 591
2010B3 - 591

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Components

#1: Protein Polyketide synthase PksL / PKS


Mass: 69044.039 Da / Num. of mol.: 2
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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 150 mM (NH4)2SO4, 15% PEG 4000 (v/v), 100 mM MES pH 6.0 mixed with 15 mg/ml protein in 150 NaCl and 20 mM HEPES pH 7.5 in 1:2 ratio

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 3.1→39.73 Å / Num. obs: 24128 / % possible obs: 94.1 % / Redundancy: 1.9 % / Net I/σ(I): 2.81

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 3.1→39.73 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.881 / Cross valid method: THROUGHOUT / ESU R Free: 0.519 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26841 1285 5.1 %RANDOM
Rwork0.2186 ---
obs0.22121 24128 94.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.801 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0 Å2-0.05 Å2
2---0.02 Å20.01 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 3.1→39.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8719 0 0 0 8719
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0198913
X-RAY DIFFRACTIONr_bond_other_d00.028377
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.96112054
X-RAY DIFFRACTIONr_angle_other_deg3.601319345
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.48451105
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.92124.621409
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.342151528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2731542
X-RAY DIFFRACTIONr_chiral_restr0.0780.21301
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110095
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021991
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_it4.9277.2174444
X-RAY DIFFRACTIONr_mcbond_other4.9277.2174443
X-RAY DIFFRACTIONr_mcangle_it7.8710.8085541
X-RAY DIFFRACTIONr_mcangle_other7.86910.8095542
X-RAY DIFFRACTIONr_scbond_it4.7387.7734469
X-RAY DIFFRACTIONr_scbond_other4.7377.7734470
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.911.4486514
X-RAY DIFFRACTIONr_long_range_B_refined11.76857.78110094
X-RAY DIFFRACTIONr_long_range_B_other11.76857.78510095
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 70032 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.101→3.181 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 82 -
Rwork0.318 1403 -
obs--75.61 %

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