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

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Basic information

Entry
Database: PDB / ID: 3hle
TitleSimvastatin Synthase (LovD), from Aspergillus terreus, S5 mutant, S76A mutant, complex with monacolin J acid
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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Chem-MJA / Monacolin J acid methylbutanoyltransferase
Similarity search - Component
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.06 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)48,6403
Polymers48,1481
Non-polymers4932
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.062, 75.321, 133.026
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 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-MJA / (3R,5R)-3,5-dihydroxy-7-[(1S,2S,6R,8S,8aR)-8-hydroxy-2,6-dimethyl-1,2,6,7,8,8a-hexahydronaphthalen-1-yl]heptanoic acid / Monacolin J acid


Mass: 338.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H30O5
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 3.02 Å3/Da / Density % sol: 59.28 %
Crystal growTemperature: 298 K / pH: 8
Details: 13% PEG 1000, 0.1M imidazole pH 8.0, 0.1 M calcium acetate, 10 mM dithiothreitol, vapor diffusion, hanging drop, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C10.9792
ROTATING ANODERIGAKU21.5418
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDMar 29, 2009
RIGAKU HTC2IMAGE PLATEMar 26, 2009
Radiation
IDProtocolScattering typeWavelength-ID
1SINGLE WAVELENGTHx-ray1
2SINGLE WAVELENGTHx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
21.54181
ReflectionResolution: 2.05→60 Å / Num. obs: 37141 / % possible obs: 99.9 % / Redundancy: 15.4 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 38.334
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.443 / % possible all: 99.8

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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 3HLD

3hld


Resolution: 2.06→49.86 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.259 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20811 1846 5 %RANDOM
Rwork0.1767 ---
obs0.17829 35223 99.85 %-
all-37069 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.683 Å2
Baniso -1Baniso -2Baniso -3
1-1.31 Å20 Å20 Å2
2---0.8 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 2.06→49.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3313 0 32 157 3502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213464
X-RAY DIFFRACTIONr_bond_other_d00.022417
X-RAY DIFFRACTIONr_angle_refined_deg1.1931.9774702
X-RAY DIFFRACTIONr_angle_other_deg4.08135849
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8875435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.77823.077169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.32915578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6851537
X-RAY DIFFRACTIONr_chiral_restr0.0690.2513
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213903
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02729
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_it1.87722125
X-RAY DIFFRACTIONr_mcbond_other02865
X-RAY DIFFRACTIONr_mcangle_it2.94433410
X-RAY DIFFRACTIONr_scbond_it2.14821339
X-RAY DIFFRACTIONr_scangle_it3.44231286
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.055→2.109 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 127 -
Rwork0.2 2559 -
obs--98.79 %
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)
11.2856-0.031-0.44740.9990.4632.43290.011-0.12880.0899-0.00230.0201-0.1276-0.07330.0509-0.03110.0386-0.00530.00290.0138-0.01270.0403-3.26816.678-12.817
20.80250.13590.01784.56041.5663.0649-0.04410.1788-0.0055-0.84340.07580.1653-0.21430.1817-0.03170.2897-0.02860.06290.0527-0.01740.08331.6188.411-38.714
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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