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

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Basic information

Entry
Database: PDB / ID: 3hlf
TitleSimvastatin Synthase (LovD), from Aspergillus terreus, S5 mutant, S76A mutant, complex with simvastatin
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
Simvastatin acid / Monacolin J acid methylbutanoyltransferase
Similarity search - Component
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 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)48,5842
Polymers48,1481
Non-polymers4371
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.470, 75.066, 131.819
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-SIM / Simvastatin acid / DIMETHYL-COMPACTIN


Mass: 436.582 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H40O6 / Comment: medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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 Å3/Da / Density % sol: 59.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG MME 550, 0.1M HEPES pH 8.0, 0.05 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: 0.9717 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9717 Å / Relative weight: 1
ReflectionResolution: 2→60 Å / Num. all: 38976 / Num. obs: 38976 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 47.3 Å2 / Rmerge(I) obs: 0.067 / Χ2: 1.108 / Net I/σ(I): 19.538
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.9 / Num. unique all: 3906 / Χ2: 0.975 / % possible all: 99.6

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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 3HLE

3hle


Resolution: 2→49.51 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.259 / WRfactor Rwork: 0.211 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.895 / SU B: 5.785 / SU ML: 0.075 / SU R Cruickshank DPI: 0.143 / SU Rfree: 0.133 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1964 5 %RANDOM
Rwork0.176 ---
all0.178 38902 --
obs0.178 38902 97.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 92.54 Å2 / Biso mean: 32.487 Å2 / Biso min: 14.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2---0.47 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 2→49.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3322 0 31 179 3532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213459
X-RAY DIFFRACTIONr_bond_other_d0.0010.022413
X-RAY DIFFRACTIONr_angle_refined_deg1.1931.984694
X-RAY DIFFRACTIONr_angle_other_deg0.86435836
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6795432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.10822.994167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74615578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6891537
X-RAY DIFFRACTIONr_chiral_restr0.0690.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213896
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02728
X-RAY DIFFRACTIONr_mcbond_it1.7322124
X-RAY DIFFRACTIONr_mcbond_other0.4832866
X-RAY DIFFRACTIONr_mcangle_it2.64833406
X-RAY DIFFRACTIONr_scbond_it2.03621335
X-RAY DIFFRACTIONr_scangle_it3.02531284
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 140 -
Rwork0.231 2574 -
all-2714 -
obs--94.14 %
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)
10.9831-0.1478-0.48541.32150.41441.75180.0146-0.0650.05890.04790.0459-0.175-0.0292-0.0024-0.06050.0045-0.0058-0.00360.0543-0.01370.0321-3.322116.5047-12.7047
20.6676-0.1003-0.33363.12090.74532.99560.05460.161-0.0099-0.67390.065-0.0034-0.1658-0.0839-0.11950.2293-0.00810.08170.0827-0.02560.09941.26287.9678-38.3587
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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