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- PDB-3gqv: Lovastatin polyketide enoyl reductase (LovC) mutant K54S with bou... -

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Basic information

Entry
Database: PDB / ID: 3gqv
TitleLovastatin polyketide enoyl reductase (LovC) mutant K54S with bound NADP
ComponentsEnoyl reductase
KeywordsOXIDOREDUCTASE / medium-chain reductase (MDR superfamily) / Rossmann fold / NADP-binding
Function / homology
Function and homology information


lovastatin nonaketide synthase / lovastatin nonaketide synthase activity / lovastatin biosynthetic process / polyketide synthase activity / polyketide biosynthetic process / oxidoreductase activity, acting on NAD(P)H / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NADPH binding / oxidoreductase activity
Similarity search - Function
: / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily ...: / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Lovastatin nonaketide synthase, enoyl reductase component lovC
Similarity search - Component
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsAmes, B.D. / Smith, P.T. / Ma, S.M. / Kaake, R. / Wong, E.W. / Wong, S.K. / Xie, X. / Li, J.W. / Vederas, J.C. / Tang, Y. / Tsai, S.-C.
CitationJournal: To be Published
Title: biosynthesis of Lovastatin: Crystal structure and biochemical studies of LOVC, A trans-acting polyketide enoyl reductase
Authors: Ames, B.D. / Smith, P.T. / Ma, S.M. / Kaake, R. / Wong, E.W. / Xie, X. / Li, J.W. / Vederas, J.C. / Tang, Y. / Tsai, S.-C.
History
DepositionMar 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enoyl reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5084
Polymers40,5811
Non-polymers9283
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.542, 44.495, 93.001
Angle α, β, γ (deg.)90.00, 101.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Enoyl reductase


Mass: 40580.789 Da / Num. of mol.: 1 / Mutation: K54S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus terreus (mold) / Gene: lovC / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y7D0
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.12 Å3/Da / Density % sol: 42.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 30% PEG 4000, 0.1 M sodium acetate, 0.2 M ammonium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9761 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2008 / Details: mirrors
RadiationMonochromator: single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9761 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. all: 34298 / Num. obs: 33414 / % possible obs: 97.5 % / Redundancy: 3.5 % / Rsym value: 0.084 / Net I/σ(I): 15.1
Reflection shellResolution: 1.74→1.8 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 2674 / Rsym value: 0.334 / % possible all: 87.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 3B70

3b70


Resolution: 1.74→35.19 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.978 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21959 1716 5 %RANDOM
Rwork0.17167 ---
obs0.17408 32577 97.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.833 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20 Å21.25 Å2
2---0.13 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.74→35.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2696 0 60 183 2939
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222867
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.9843930
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.445361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.23323.554121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.51515428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1241520
X-RAY DIFFRACTIONr_chiral_restr0.0960.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022206
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.21246
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21948
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2184
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.265
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1070.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2171.51815
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.83322881
X-RAY DIFFRACTIONr_scbond_it3.85931191
X-RAY DIFFRACTIONr_scangle_it3.8874.51043
X-RAY DIFFRACTIONr_rigid_bond_restr3.97933006
X-RAY DIFFRACTIONr_sphericity_free5.1633183
X-RAY DIFFRACTIONr_sphericity_bonded3.39232788
LS refinement shellResolution: 1.74→1.78 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 97 -
Rwork0.203 1988 -
obs-2625 79.43 %

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