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- PDB-3slk: Structure of ketoreductase and enoylreductase didomain from modul... -

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Basic information

Entry
Database: PDB / ID: 3slk
TitleStructure of ketoreductase and enoylreductase didomain from modular polyketide synthase
ComponentsPolyketide synthase extender module 2
KeywordsOXIDOREDUCTASE / Rossmann Fold / NADPH
Function / homology
Function and homology information


phosphopantetheine binding / antibiotic biosynthetic process / transferase activity / oxidoreductase activity / nucleotide binding / zinc ion binding
Similarity search - Function
Rossmann fold - #11460 / Quinone oxidoreductase/zeta-crystallin, conserved site / : / Quinone oxidoreductase / zeta-crystallin signature. / Zinc-binding dehydrogenase / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain ...Rossmann fold - #11460 / Quinone oxidoreductase/zeta-crystallin, conserved site / : / Quinone oxidoreductase / zeta-crystallin signature. / Zinc-binding dehydrogenase / Polyketide synthase, docking domain / Erythronolide synthase docking domain / 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 / Malonyl-CoA ACP transacylase, ACP-binding / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / 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 / GroES-like superfamily / Thiolase-like / 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 / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Polyketide synthase extender module 2
Similarity search - Component
Biological speciesSaccharopolyspora spinosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsZheng, J. / Gay, D.C. / Keatinge-Clay, A.T.
CitationJournal: Nat.Chem.Biol. / Year: 2012
Title: Divergence of multimodular polyketide synthases revealed by a didomain structure.
Authors: Zheng, J. / Gay, D.C. / Demeler, B. / White, M.A. / Keatinge-Clay, A.T.
History
DepositionJun 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Sep 5, 2012Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyketide synthase extender module 2
B: Polyketide synthase extender module 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,1199
Polymers166,8492
Non-polymers3,2707
Water0
1
A: Polyketide synthase extender module 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1085
Polymers83,4251
Non-polymers1,6834
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polyketide synthase extender module 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,0114
Polymers83,4251
Non-polymers1,5873
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.104, 110.195, 202.857
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 extender module 2


Mass: 83424.555 Da / Num. of mol.: 2
Fragment: ketoreductase and enoylreductase didomain (UNP residues 1216-1989)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharopolyspora spinosa (bacteria) / Gene: spnB / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9ALM5, 3-oxoacyl-[acyl-carrier-protein] reductase, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4

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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: 2.45 Å3/Da / Density % sol: 49.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 17% poly(acrylic acid) 5100, 0.4 M magnesium sulfate, 0.1 M HEPES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONALS 8.2.110.9999
SYNCHROTRONALS 5.0.220.9645, 0.9797, 0.9796
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDMay 21, 2010
ADSC QUANTUM 315r2CCDJun 28, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal, Si(111)SINGLE WAVELENGTHMx-ray1
2Double-crystal, Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.99991
20.96451
30.97971
40.97961
ReflectionResolution: 2.9→50 Å / Num. all: 35368 / Num. obs: 35220 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 16.2
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.723 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.912 / SU B: 19.353 / SU ML: 0.343 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R Free: 0.464 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25584 1698 5.1 %RANDOM
Rwork0.20982 ---
obs0.21219 31804 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.931 Å2
Baniso -1Baniso -2Baniso -3
1--3.48 Å20 Å2-0 Å2
2--5.63 Å20 Å2
3----2.15 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11010 0 207 0 11217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01911448
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0142.00115668
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.22751490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.21322.991448
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.912151692
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3315106
X-RAY DIFFRACTIONr_chiral_restr0.0750.21823
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0218702
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.7571.57416
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4211834
X-RAY DIFFRACTIONr_scbond_it1.77634066
X-RAY DIFFRACTIONr_scangle_it3.084.53882
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 100 -
Rwork0.295 2062 -
obs--96.35 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.1330.0907-0.22820.22060.04940.8095-0.09-0.0014-0.0049-0.17050.04880.00420.0279-0.06310.04110.1384-0.0396-0.01060.1219-0.02340.09849.9088103.582347.8938
20.0976-0.0388-0.15930.18460.32570.75120.0624-0.0124-0.0199-0.0366-0.02080.0036-0.05960.0328-0.04170.09670.0603-0.03090.105-0.06010.13199.044747.5806-6.8303
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 751
2X-RAY DIFFRACTION2B1 - 751

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