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

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Basic information

Entry
Database: PDB / ID: 3hlb
TitleSimvastatin Synthase (LovD) from Aspergillus terreus, unliganded, selenomethionyl derivative
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: 2.5 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
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 ...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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,68317
Polymers192,4354
Non-polymers1,24913
Water37821
1
A: Transesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4935
Polymers48,1091
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3974
Polymers48,1091
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Transesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3974
Polymers48,1091
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Transesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3974
Polymers48,1091
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)209.475, 85.215, 104.047
Angle α, β, γ (deg.)90.000, 117.480, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D

NCS domain segments:

Refine code: 4

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALAARGARGAA10 - 9229 - 111
211ALAALAARGARGBB10 - 9229 - 111
311ALAALAARGARGCC10 - 9229 - 111
411ALAALAARGARGDD10 - 9229 - 111
121GLYGLYALAALAAA204 - 408223 - 427
221GLYGLYALAALABB204 - 408223 - 427
321GLYGLYALAALACC204 - 408223 - 427
421GLYGLYALAALADD204 - 408223 - 427
112GLYGLYTHRTHRAA93 - 203112 - 222
212GLYGLYTHRTHRBB93 - 203112 - 222
312GLYGLYTHRTHRCC93 - 203112 - 222
412GLYGLYTHRTHRDD93 - 203112 - 222

NCS ensembles :
ID
1
2

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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
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.14 Å3/Da / Density % sol: 42.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 22% PEG 3350, 0.1M Bis-Tris pH 6.5, 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 Å
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: 2.5→54.39 Å / Num. all: 50258 / Num. obs: 50258 / % possible obs: 89.9 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 62.8 Å2 / Rmerge(I) obs: 0.143 / Χ2: 1.083 / Net I/σ(I): 10.24
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 3 / Num. unique all: 2603 / Χ2: 1.022 / % possible all: 46.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.2 Å46.14 Å
Translation4.2 Å46.14 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.2phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3HL9

3hl9


Resolution: 2.5→54.39 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.886 / WRfactor Rfree: 0.295 / WRfactor Rwork: 0.252 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.78 / SU B: 32.917 / SU ML: 0.326 / SU R Cruickshank DPI: 0.337 / SU Rfree: 0.395 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.395 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29 2518 5 %RANDOM
Rwork0.248 ---
obs0.25 50246 89.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 98.86 Å2 / Biso mean: 51.757 Å2 / Biso min: 32.14 Å2
Baniso -1Baniso -2Baniso -3
1--1.75 Å20 Å2-3.33 Å2
2--0.14 Å20 Å2
3----1.46 Å2
Refinement stepCycle: LAST / Resolution: 2.5→54.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12547 0 65 21 12633
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02212865
X-RAY DIFFRACTIONr_bond_other_d0.0010.028921
X-RAY DIFFRACTIONr_angle_refined_deg0.9951.97617431
X-RAY DIFFRACTIONr_angle_other_deg0.823321578
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.52151593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.24423.344625
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.098152167
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.93515130
X-RAY DIFFRACTIONr_chiral_restr0.0560.21874
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02114427
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022647
X-RAY DIFFRACTIONr_mcbond_it0.81327950
X-RAY DIFFRACTIONr_mcbond_other0.17223237
X-RAY DIFFRACTIONr_mcangle_it1.401312728
X-RAY DIFFRACTIONr_scbond_it0.79524915
X-RAY DIFFRACTIONr_scangle_it1.28334703
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3725MEDIUM POSITIONAL0.260.5
1B3725MEDIUM POSITIONAL0.250
1C3725MEDIUM POSITIONAL0.230
1D3725MEDIUM POSITIONAL0.280
1A3725MEDIUM THERMAL0.222
1B3725MEDIUM THERMAL0.210
1C3725MEDIUM THERMAL0.20
1D3725MEDIUM THERMAL0.220
2A1479MEDIUM POSITIONAL0.20.5
2B1479MEDIUM POSITIONAL0.210
2C1479MEDIUM POSITIONAL0.230
2D1479MEDIUM POSITIONAL0.290
2A1479MEDIUM THERMAL0.192
2B1479MEDIUM THERMAL0.180
2C1479MEDIUM THERMAL0.190
2D1479MEDIUM THERMAL0.180
LS refinement shellResolution: 2.503→2.568 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 91 -
Rwork0.356 1566 -
all-1657 -
obs--40.18 %
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)
11.914-0.2708-0.07372.5987-0.14382.4372-0.13050.2687-0.0855-0.19960.0593-0.26940.11520.0190.0712-0.1912-0.02540.0055-0.0876-0.0747-0.2168-2.3424-3.282837.6889
22.2110.32930.49472.9653-0.26771.8289-0.07990.12710.1958-0.25970.0755-0.2026-0.04790.20350.0044-0.1781-0.0495-0.0039-0.0606-0.0241-0.2516-6.908636.157330.2388
32.35810.1511.34314.4719-0.20583.69120.2370.2636-0.204-0.5041-0.0177-0.1861-0.035-0.2402-0.2193-0.08780.0839-0.046-0.2332-0.0304-0.137727.7651-21.8812.3448
42.5179-0.09160.77943.03180.42992.7439-0.0439-0.3101-0.040.0162-0.0742-0.3538-0.14030.0830.118-0.1239-0.0709-0.1007-0.22550.0789-0.17839.740212.080221.3976
52.2792-0.16161.10164.8955-0.47131.9732-0.07110.00610.04270.5297-0.0079-0.1704-0.19120.02550.0791-0.03180.014-0.1692-0.0804-0.0524-0.21620.934413.997557.4232
61.58530.05170.37975.53010.15212.0022-0.03090.2396-0.0576-0.35010.06080.5630.1835-0.0459-0.0299-0.0304-0.0622-0.17320.03590.0027-0.2618-23.405818.945218.8547
72.91270.76180.9892.62690.16535.25350.1819-0.6162-0.13630.6926-0.1516-0.20560.0479-0.2634-0.03030.0174-0.0295-0.2026-0.1270.123-0.081834.2227-23.006728.2335
83.36550.26591.61763.93921.64144.5774-0.04050.0253-0.0047-0.2129-0.12110.3392-0.1145-0.53550.16160.10130.1555-0.1889-0.1461-0.028-0.2119.937713.48143.3443
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 92
2X-RAY DIFFRACTION1A204 - 413
3X-RAY DIFFRACTION2B10 - 92
4X-RAY DIFFRACTION2B204 - 413
5X-RAY DIFFRACTION3C10 - 92
6X-RAY DIFFRACTION3C204 - 413
7X-RAY DIFFRACTION4D10 - 92
8X-RAY DIFFRACTION4D204 - 413
9X-RAY DIFFRACTION5A93 - 203
10X-RAY DIFFRACTION6B93 - 203
11X-RAY DIFFRACTION7C93 - 203
12X-RAY DIFFRACTION8D93 - 203

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