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- PDB-3hl9: Simvastatin Synthase (LovD) from Aspergillus terreus, unliganded -

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Basic information

Entry
Database: PDB / ID: 3hl9
TitleSimvastatin Synthase (LovD) from Aspergillus terreus, 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: 3.4 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
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transesterase
B: Transesterase
C: Transesterase
D: Transesterase


Theoretical massNumber of molelcules
Total (without water)192,4354
Polymers192,4354
Non-polymers00
Water00
1
A: Transesterase


Theoretical massNumber of molelcules
Total (without water)48,1091
Polymers48,1091
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Transesterase


Theoretical massNumber of molelcules
Total (without water)48,1091
Polymers48,1091
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Transesterase


Theoretical massNumber of molelcules
Total (without water)48,1091
Polymers48,1091
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Transesterase


Theoretical massNumber of molelcules
Total (without water)48,1091
Polymers48,1091
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.721, 79.744, 104.115
Angle α, β, γ (deg.)94.110, 91.560, 106.790
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 1 / Auth seq-ID: 10 - 408 / Label seq-ID: 29 - 427

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
Transesterase / LovD


Mass: 48108.629 Da / Num. of mol.: 4 / Mutation: C40A, C60N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus terreus (mold) / Gene: lovD / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)with bioH knockout / References: UniProt: Q9Y7D1

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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: 2.33 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 298 K / pH: 7
Details: 20% PEG 3350, 0.1M HEPES pH 7.0, 0.25 M ammonium sulfate, 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: 0.9793
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 23, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.4→76.03 Å / Num. obs: 23701 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 10.8 Å2 / Rmerge(I) obs: 0.235 / Net I/σ(I): 4.974
Reflection shellResolution: 3.4→3.66 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 2.9 / % possible all: 98.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
XSCALEdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1IC9

1ic9


Resolution: 3.4→76.03 Å / Cor.coef. Fo:Fc: 0.868 / Cor.coef. Fo:Fc free: 0.811 / Occupancy max: 1 / Occupancy min: 1 / SU B: 83.138 / SU ML: 0.59 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.708 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1216 5.1 %RANDOM
Rwork0.231 ---
obs0.233 23673 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 6.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å2-3.61 Å2-2.28 Å2
2--0.86 Å22.1 Å2
3----2.16 Å2
Refinement stepCycle: LAST / Resolution: 3.4→76.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12328 0 0 0 12328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02212588
X-RAY DIFFRACTIONr_bond_other_d0.0020.028776
X-RAY DIFFRACTIONr_angle_refined_deg1.2571.97217044
X-RAY DIFFRACTIONr_angle_other_deg0.933321232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.551564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.84523.289608
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.61152136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.03615128
X-RAY DIFFRACTIONr_chiral_restr0.0690.21848
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02114124
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022592
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_it0.58627812
X-RAY DIFFRACTIONr_mcbond_other0.12623180
X-RAY DIFFRACTIONr_mcangle_it0.954312508
X-RAY DIFFRACTIONr_scbond_it0.52724776
X-RAY DIFFRACTIONr_scangle_it0.78334536
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 5204 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Atight positional0.030.05
Btight positional0.030.05
Ctight positional0.030.05
Dtight positional0.030.05
Atight thermal0.060.5
Btight thermal0.060.5
Ctight thermal0.050.5
Dtight thermal0.050.5
LS refinement shellResolution: 3.4→3.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 95 -
Rwork0.319 1574 -
obs--94.83 %
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)
11.8362-0.39920.97651.3507-0.21162.51520.0151-0.0379-0.11870.0928-0.03350.0057-0.0183-0.09340.01840.0178-0.00790.01270.0077-0.00810.03680.942-1.6590.1794
21.69910.38910.45632.1619-0.61982.89750.0945-0.1277-0.05320.1687-0.0668-0.0099-0.1963-0.0558-0.02770.0411-0.01380.01870.0137-0.00530.0319-12.959-34.2849-2.8425
31.72470.12050.70281.6355-0.05444.03570.04230.0307-0.0076-0.1671-0.0081-0.04820.04790.0003-0.03420.0384-0.00090.03980.02510.01970.0895-40.1781-29.2379-47.4844
42.97370.06282.0411.9166-0.54394.0875-0.2192-0.19250.19530.2162-0.0406-0.1021-0.405-0.10210.25980.0949-0.0149-0.00820.0517-0.00340.1167-33.27814.541-54.7463
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 408
2X-RAY DIFFRACTION2B10 - 408
3X-RAY DIFFRACTION3C10 - 408
4X-RAY DIFFRACTION4D10 - 408

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