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- PDB-4lcm: Simvastatin Synthase (LOVD), from Aspergillus Terreus, LovD9 muta... -

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Basic information

Entry
Database: PDB / ID: 4lcm
TitleSimvastatin Synthase (LOVD), from Aspergillus Terreus, LovD9 mutant (simh9014)
ComponentsTransesterase
KeywordsTRANSFERASE / laboratory-directed evolution / Transesterase
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: 3.19 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)189,0844
Polymers189,0844
Non-polymers00
Water21612
1
A: Transesterase


Theoretical massNumber of molelcules
Total (without water)47,2711
Polymers47,2711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Transesterase


Theoretical massNumber of molelcules
Total (without water)47,2711
Polymers47,2711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Transesterase


Theoretical massNumber of molelcules
Total (without water)47,2711
Polymers47,2711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Transesterase


Theoretical massNumber of molelcules
Total (without water)47,2711
Polymers47,2711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.310, 83.940, 99.200
Angle α, β, γ (deg.)102.560, 89.020, 107.640
Int Tables number1
Space group name H-MP1
DetailsThe biological unit is a monomer. There are four biological units in the asymmetric unit (chains A,B,C,D).

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Components

#1: Protein
Transesterase


Mass: 47271.008 Da / Num. of mol.: 4
Mutation: I4N A9V K26E R28S I35L C40A N43R C60N D96R S109C A123P M157V S164G S172N L174F A178V N191G L192I Q241M A247S R250K S256T A261H G275S Q297G L335M L361M V370I A383V N391S 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 18% PEG-3350, 0.1 M Bis-Tris pH 5.5, 0.2 M MgCl2, 10mM 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-E / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.19→19.66 Å / Num. all: 25955 / Num. obs: 25955 / % possible obs: 92.1 % / Observed criterion σ(I): -3 / Redundancy: 1.8 % / Biso Wilson estimate: 37.052 Å2 / Rmerge(I) obs: 0.175 / Net I/σ(I): 4.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
3.19-3.270.67913243184989.2
3.27-3.360.5641.253309187892
3.36-3.460.4381.663187178691.5
3.46-3.560.4041.843217180192.9
3.56-3.680.2762.913062170091.3
3.68-3.810.2612.923031168092.7
3.81-3.950.2363.342878158792.8
3.95-4.110.1853.952869156692.9
4.11-4.30.1574.482754151794.6
4.3-4.510.145.332597142793.8
4.51-4.750.126.122510137793.6
4.75-5.040.1425.332373129694.7
5.04-5.390.1195.642195120293
5.39-5.820.1465.232050113093.6
5.82-6.370.1345.661881102892.8
6.37-7.130.1086.99169995993.6
7.13-8.230.06710.4150681493.3
8.23-10.080.0416.22126066289.8
10.08-14.250.0319.64102853489.3
14.250.02918.231116254

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å19.67 Å
Translation3.5 Å19.67 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HLC

3hlc


Resolution: 3.19→19.66 Å / Cor.coef. Fo:Fc: 0.8573 / Cor.coef. Fo:Fc free: 0.7961 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1302 5.02 %RANDOM
Rwork0.2077 ---
all0.2099 25938 --
obs0.2099 25938 --
Displacement parametersBiso max: 148.28 Å2 / Biso mean: 50.781 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--7.8942 Å28.5905 Å25.1409 Å2
2--12.7378 Å210.2425 Å2
3----4.8435 Å2
Refine analyzeLuzzati coordinate error obs: 0.566 Å
Refinement stepCycle: LAST / Resolution: 3.19→19.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12344 0 0 12 12356
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4648SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes316HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1844HARMONIC5
X-RAY DIFFRACTIONt_it12608HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1572SEMIHARMONIC5
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_contact15466SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d12608HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg17056HARMONIC21.26
X-RAY DIFFRACTIONt_omega_torsion2.72
X-RAY DIFFRACTIONt_other_torsion21.75
LS refinement shellResolution: 3.19→3.32 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2371 152 5.23 %
Rwork0.2315 2757 -
all0.2318 2909 -
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)
12.822-0.141.47182.9959-0.67312.59660.03740.0283-0.0337-0.03090.00590.14640.22890.0077-0.0433-0.208-0.05370.0106-0.17940.1796-0.12654.3177-24.7084-3.2352
21.7298-0.36581.61962.7867-0.57113.0826-0.08990.0077-0.03970.2994-0.02-0.1611-0.1277-0.05160.1099-0.0766-0.0631-0.0382-0.17940.2443-0.189125.0869-33.396243.7179
31.40420.64381.05642.7198-0.57623.3386-0.1226-0.02160.138-0.42480.18010.09880.0378-0.1728-0.0575-0.065-0.043-0.0311-0.23370.2283-0.139216.101-71.6747.1232
41.1050.26430.5112.2868-0.88272.96290.1546-0.01750.04840.2062-0.1072-0.1664-0.02830.1068-0.0474-0.1278-0.0503-0.0764-0.16210.18-0.0484-10.5896-60.7286-9.4324
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A12 - 413
2X-RAY DIFFRACTION2{ B|* }B12 - 413
3X-RAY DIFFRACTION3{ C|* }C12 - 413
4X-RAY DIFFRACTION4{ D|* }D12 - 413

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