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

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Basic information

Entry
Database: PDB / ID: 3hlg
TitleSimvastatin Synthase (LovD), from Aspergillus terreus, S5 mutant, S76A mutant, complex with lovastatin
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
Chem-LVA / Monacolin J acid methylbutanoyltransferase
Similarity search - Component
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.01 Å
AuthorsSawaya, M.R. / Yeates, T.O. / 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 1.4Sep 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

Downloads & links

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Assembly

Deposited unit
A: Transesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5702
Polymers48,1481
Non-polymers4231
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.042, 75.189, 131.696
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transesterase / LovD


Mass: 48147.660 Da / Num. of mol.: 1 / Mutation: C40A C60N D12G K26E A86V H161Y A190T G275S S76A
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-LVA / (3R,5R)-7-((1R,2R,6S,8R,8AS)-2,6-DIMETHYL-8-{[(2R)-2-METHYLBUTANOYL]OXY}-1,2,6,7,8,8A-HEXAHYDRONAPHTHALEN-1-YL)-3,5-DIHYDROXYHEPTANOIC ACID


Mass: 422.555 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H38O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 3.04 Å3/Da / Density % sol: 59.48 %
Crystal growTemperature: 298 K / pH: 8
Details: 15% PEG MME 550, 0.1M HEPES pH 8.0, 0.1 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: 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→60 Å / Num. obs: 39042 / % possible obs: 98.5 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 13.333
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.411 / % possible all: 99.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3HLF

3hlf


Resolution: 2.01→46.42 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.859 / SU ML: 0.075 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.189 1951 5 %RANDOM
Rwork0.162 ---
obs0.163 38956 97.9 %-
all-38956 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2---0.1 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.01→46.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3322 0 30 230 3582
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213449
X-RAY DIFFRACTIONr_bond_other_d0.0010.022402
X-RAY DIFFRACTIONr_angle_refined_deg1.1931.9794678
X-RAY DIFFRACTIONr_angle_other_deg0.85835812
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7395430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.71123.072166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76115575
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2561536
X-RAY DIFFRACTIONr_chiral_restr0.0690.2509
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213884
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02723
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_it1.72722121
X-RAY DIFFRACTIONr_mcbond_other0.4782865
X-RAY DIFFRACTIONr_mcangle_it2.67733400
X-RAY DIFFRACTIONr_scbond_it2.02621328
X-RAY DIFFRACTIONr_scangle_it3.09731275
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.01→2.06 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 145 -
Rwork0.183 2526 -
obs--91.6 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7338-0.1129-0.30760.65680.30331.30340.0094-0.06370.0417-0.00360.0356-0.096-0.0287-0.004-0.0450.006-0.00580.00640.0154-0.00790.0543-3.214216.5719-12.7272
21.0248-0.3177-0.26182.13530.27042.09370.09340.18640.0059-0.42880.0149-0.0433-0.0633-0.0531-0.10830.1471-0.00840.06440.0401-0.01170.05921.09498.1136-38.3269
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-11 - 92
2X-RAY DIFFRACTION1A204 - 413
3X-RAY DIFFRACTION2A93 - 203

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