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- PDB-3hlc: Simvastatin Synthase (LovD) from Aspergillus terreus, S5 mutant, ... -

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Basic information

Entry
Database: PDB / ID: 3hlc
TitleSimvastatin Synthase (LovD) from Aspergillus terreus, S5 mutant, unliganded
ComponentsTransesterase
KeywordsTRANSFERASE / alpha/beta hydrolase fold
Function / homology
Function and homology information


monacolin J acid methylbutanoate transferase / lovastatin biosynthetic process / polyketide synthase activity / polyketide biosynthetic process / acyltransferase activity / antibiotic biosynthetic process / defense response to fungus / hydrolase activity
Similarity search - Function
: / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Monacolin J acid methylbutanoyltransferase
Similarity search - Component
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsSawaya, M.R. / Yeates, T.O. / Laidman, J. / Pashkov, I. / Gao, X. / Tang, Y.
CitationJournal: Chem.Biol. / Year: 2009
Title: Directed evolution and structural characterization of a simvastatin synthase
Authors: Gao, X. / Xie, X. / Pashkov, I. / Sawaya, M.R. / Laidman, J. / Zhang, W. / Cacho, R. / Yeates, T.O. / Tang, Y.
History
DepositionMay 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 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 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4503
Polymers48,1641
Non-polymers2862
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.154, 75.031, 131.621
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a monomer. The biological unit is the asymmetric unit (chain A).

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Components

#1: Protein Transesterase / LovD


Mass: 48163.660 Da / Num. of mol.: 1 / Mutation: C40A, C60N, D12G, K26E, A86V, H161Y, A190T, G275S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus terreus (mold) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)with bioH knockout / References: UniProt: Q9Y7D1
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.98 Å3/Da / Density % sol: 58.74 %
Crystal growTemperature: 298 K / pH: 7.5
Details: 40% PEG 400, 0.1M HEPES pH 7.5, 0.25 M magnesium chloride, 10 mM dithiothreitol, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9794
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 29, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→49.45 Å / Num. obs: 39600 / % possible obs: 99.9 % / Redundancy: 11.6 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 46.972
Reflection shellResolution: 2→2.07 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.429 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→49.45 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.773 / SU ML: 0.076 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1987 5 %RANDOM
Rwork0.18 ---
obs0.181 39526 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å20 Å2
2---1.23 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→49.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3257 0 19 150 3426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213380
X-RAY DIFFRACTIONr_bond_other_d0.0010.022375
X-RAY DIFFRACTIONr_angle_refined_deg1.1991.9734576
X-RAY DIFFRACTIONr_angle_other_deg0.8635735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7625422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.34822.848165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.08815568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1341538
X-RAY DIFFRACTIONr_chiral_restr0.070.2493
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213791
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02710
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_it1.79522079
X-RAY DIFFRACTIONr_mcbond_other0.4652846
X-RAY DIFFRACTIONr_mcangle_it2.82833336
X-RAY DIFFRACTIONr_scbond_it1.93121301
X-RAY DIFFRACTIONr_scangle_it2.95331236
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 143 -
Rwork0.204 2694 -
obs--98.4 %
Refinement TLS params.Method: refined / Origin x: -1.6041 Å / Origin y: 13.4023 Å / Origin z: -21.2096 Å
111213212223313233
T0.0296 Å2-0.0082 Å20.0228 Å2-0.0061 Å2-0.0016 Å2--0.0335 Å2
L0.8658 °2-0.0418 °2-0.4325 °2-1.2238 °20.3381 °2--2.0312 °2
S-0.0197 Å °0.0128 Å °0.0238 Å °-0.1406 Å °0.0081 Å °-0.1736 Å °-0.0139 Å °0.0451 Å °0.0116 Å °

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