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- PDB-4lcl: Simvastatin Synthase (LOVD), from Aspergillus Terreus, LovD6 muta... -

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Basic information

Entry
Database: PDB / ID: 4lcl
TitleSimvastatin Synthase (LOVD), from Aspergillus Terreus, LovD6 mutant (simh6208)
ComponentsTransesterase
KeywordsTRANSFERASE / laboratory-directed evolution / Transesterase
Function / homology
Function and homology information


monacolin J acid methylbutanoate transferase / polyketide synthase activity / lovastatin biosynthetic process / 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
ISOPROPYL ALCOHOL / Monacolin J acid methylbutanoyltransferase
Similarity search - Component
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsGao, X. / Sawaya, M.R. / Yeates, T.O. / Tang, Y.
CitationJournal: Nat.Chem.Biol. / Year: 2014
Title: The role of distant mutations and allosteric regulation on LovD active site dynamics.
Authors: Jimenez-Oses, G. / Osuna, S. / Gao, X. / Sawaya, M.R. / Gilson, L. / Collier, S.J. / Huisman, G.W. / Yeates, T.O. / Tang, Y. / Houk, K.N.
History
DepositionJun 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2May 28, 2014Group: Database references
Revision 1.3Jun 4, 2014Group: Database references
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software
Revision 1.5Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transesterase
B: Transesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9084
Polymers96,7882
Non-polymers1202
Water6,900383
1
A: Transesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4542
Polymers48,3941
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Transesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4542
Polymers48,3941
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.800, 76.390, 113.760
Angle α, β, γ (deg.)90.000, 93.910, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is a monomer. There are two biological units in the asymmetric unit (chain A and chain B).

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Components

#1: Protein Transesterase


Mass: 48394.133 Da / Num. of mol.: 2
Mutation: A9V K26E C40A N43R C60N A123P M157V S164G S172N A178L N191G L192I Q241M A247S R250K G275S Q297E L361M V370I A383V H404K
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) / References: UniProt: Q9Y7D1
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 1.96 Å3/Da / Density % sol: 37.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 18% PEG-4000, 50mM sodium citrate pH 5.6, 16% propanol, 1mM DTT, 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: 0.9641 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9641 Å / Relative weight: 1
ReflectionResolution: 1.8→18.1 Å / Num. all: 69030 / Num. obs: 69030 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 22.45 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 21.01
Reflection shell
Resolution (Å)Mean I/σ(I) obsRsym valueDiffraction-ID% possible allNum. unique all
1.8-1.853.1751.5199.5
3.29-3.650.492.1199.1
3.6-4.6552.552199
4.65-5.6954.141.7199.3
5.69-8.0553.961.8199.3
8.05-18.157.271.6195.6787

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å45.55 Å
Translation3 Å45.55 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.3.0phasing
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
XSCALEdata scaling
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HLC

3hlc


Resolution: 1.8→18.1 Å / Cor.coef. Fo:Fc: 0.9555 / Cor.coef. Fo:Fc free: 0.9471 / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.191 3448 5 %RANDOM
Rwork0.1672 ---
obs0.1684 68966 99.48 %-
all-68966 --
Displacement parametersBiso max: 123.68 Å2 / Biso mean: 28.0407 Å2 / Biso min: 8.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.8964 Å20 Å20.2552 Å2
2---1.1644 Å20 Å2
3---2.0608 Å2
Refine analyzeLuzzati coordinate error obs: 0.208 Å
Refinement stepCycle: LAST / Resolution: 1.8→18.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6350 0 8 383 6741
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2319SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes170HARMONIC2
X-RAY DIFFRACTIONt_gen_planes964HARMONIC5
X-RAY DIFFRACTIONt_it6541HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion817SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8121SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6541HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8860HARMONIC21.02
X-RAY DIFFRACTIONt_omega_torsion3.74
X-RAY DIFFRACTIONt_other_torsion15.51
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2168 255 5.01 %
Rwork0.1977 4834 -
all0.1986 5089 -
obs--99.48 %
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)
10.7766-0.1055-0.00310.7517-0.16580.96150.010.12420.0214-0.09940.01320.0188-0.0083-0.0388-0.0231-0.05880.00870.0035-0.06210.0053-0.058516.53524.486411.3501
21.2158-0.1173-0.09221.1346-0.37161.33790.0374-0.3267-0.00450.13670.03830.0349-0.0160.0081-0.0757-0.1178-0.00860.0043-0.05-0.0043-0.111612.552554.757244.9126
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A-10 - 413
2X-RAY DIFFRACTION2{ B|* }B-9 - 413

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