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- PDB-5ktk: Ketoreductase from module 3 of the bacillaene synthase from Bacil... -

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Basic information

Entry
Database: PDB / ID: 5ktk
TitleKetoreductase from module 3 of the bacillaene synthase from Bacillus subtilis 168
ComponentsPolyketide synthase PksJ
KeywordsOXIDOREDUCTASE / Bacillaene polyketide ketoreductase
Function / homology
Function and homology information


: / DIM/DIP cell wall layer assembly / fatty acid synthase activity / secondary metabolite biosynthetic process / ligase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process / plasma membrane / cytoplasm
Similarity search - Function
: / : / Polyketide synthase dehydratase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / PKS_PP_betabranch / Condensation domain / Condensation domain / Polyketide synthase dehydratase N-terminal domain / Amino acid adenylation domain ...: / : / Polyketide synthase dehydratase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / PKS_PP_betabranch / Condensation domain / Condensation domain / Polyketide synthase dehydratase N-terminal domain / Amino acid adenylation 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 / ANL, N-terminal domain / PKS_KR / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / Chloramphenicol acetyltransferase-like domain superfamily / AMP-binding, conserved site / Putative AMP-binding domain signature. / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / 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 / 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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Polyketide synthase PksJ
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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)2616061650 United States
CitationJournal: To Be Published
Title: Ketoreductase from module 3 of the bacillaene synthase from Bacillus subtilis 168
Authors: Wagner, D.T. / Gay, D.C. / Keatinge-Clay, A.T.
History
DepositionJul 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyketide synthase PksJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0032
Polymers58,2581
Non-polymers7451
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-3 kcal/mol
Surface area19240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.098, 84.869, 134.298
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Polyketide synthase PksJ / PKS


Mass: 58257.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: pksJ, pksK, BSU17180 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P40806
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O

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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: 2.25 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 9 mg/mL PksKR3, 150 mM NaCl, 10mM HEPES, pH 7.5 with 1 uL crystallization buffer (sodium citrate, 0.1 M HEPES pH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Nov 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→71.74 Å / Num. obs: 37725 / % possible obs: 97.1 % / Redundancy: 6.4 % / Net I/σ(I): 21.75

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J1Q

4j1q


Resolution: 1.98→71.74 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.946 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23133 1819 5 %RANDOM
Rwork0.20675 ---
obs0.208 34894 97.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.432 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.98→71.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3560 0 48 155 3763
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193686
X-RAY DIFFRACTIONr_bond_other_d00.023468
X-RAY DIFFRACTIONr_angle_refined_deg1.6021.9695001
X-RAY DIFFRACTIONr_angle_other_deg3.69937974
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1375449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93123.846169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.11215625
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9251526
X-RAY DIFFRACTIONr_chiral_restr0.0980.2556
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024135
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02857
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_it3.5062.1941805
X-RAY DIFFRACTIONr_mcbond_other3.5072.1931804
X-RAY DIFFRACTIONr_mcangle_it4.933.2692251
X-RAY DIFFRACTIONr_mcangle_other4.9293.272252
X-RAY DIFFRACTIONr_scbond_it4.5692.7331881
X-RAY DIFFRACTIONr_scbond_other4.5672.7331882
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5913.8872751
X-RAY DIFFRACTIONr_long_range_B_refined9.03326.7754095
X-RAY DIFFRACTIONr_long_range_B_other9.03626.5044059
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.975→2.027 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 119 -
Rwork0.293 2277 -
obs--87.19 %

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