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- PDB-6ad3: Structural characterization of the condensation domain from Monac... -

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Basic information

Entry
Database: PDB / ID: 6ad3
TitleStructural characterization of the condensation domain from Monacolin K polyketide synthase MokA
ComponentsLovastatin nonaketide synthase mokA
KeywordsBIOSYNTHETIC PROTEIN / polyketide synthease / condensation domain / nonribosomal peptide synthetases
Function / homology
Function and homology information


lovastatin nonaketide synthase / lovastatin nonaketide synthase activity / toxin biosynthetic process / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / methyltransferase activity / fatty acid biosynthetic process / methylation / oxidoreductase activity
Similarity search - Function
Methyltransferase type 12 / Methyltransferase domain / : / Polyketide synthase dehydratase N-terminal domain / Condensation domain / Condensation domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain ...Methyltransferase type 12 / Methyltransferase domain / : / Polyketide synthase dehydratase N-terminal domain / Condensation domain / Condensation domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / Polyketide synthase, dehydratase domain superfamily / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / Chloramphenicol acetyltransferase-like domain superfamily / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / PKS_KR / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Lovastatin nonaketide synthase mokA
Similarity search - Component
Biological speciesMonascus pilosus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.79 Å
AuthorsWang, L. / Zheng, J.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31370101 China
National Natural Science Foundation of China31570056 China
CitationJournal: Synth Syst Biotechnol / Year: 2019
Title: Crystal structure of the condensation domain from lovastatin polyketide synthase.
Authors: Wang, L. / Yuan, M. / Zheng, J.
History
DepositionJul 30, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lovastatin nonaketide synthase mokA


Theoretical massNumber of molelcules
Total (without water)57,4461
Polymers57,4461
Non-polymers00
Water4,684260
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.101, 64.042, 173.196
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein Lovastatin nonaketide synthase mokA / Monacolin K biosynthesis protein A


Mass: 57446.180 Da / Num. of mol.: 1 / Mutation: R153W
Source method: isolated from a genetically manipulated source
Details: Monascus pilosus / Source: (gene. exp.) Monascus pilosus (fungus) / Gene: mokA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q3S2T9, lovastatin nonaketide synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, potassium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 54424 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.032 / Rrim(I) all: 0.082 / Χ2: 0.445 / Net I/σ(I): 4.5 / Num. measured all: 356651
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.79-1.826.60.42227270.9190.1760.4580.438100
1.82-1.856.80.36426240.9370.150.3940.462100
1.85-1.896.70.31527070.9580.1310.3420.4699.9
1.89-1.936.70.27826340.9680.1160.3020.464100
1.93-1.976.60.24727070.9740.1040.2690.474100
1.97-2.026.50.20826700.9760.0880.2260.47999.9
2.02-2.0760.17626890.980.0780.1930.464100
2.07-2.126.70.16127150.9880.0670.1750.484100
2.12-2.186.80.14626690.9890.060.1580.479100
2.18-2.266.80.12826900.9890.0530.1390.478100
2.26-2.346.60.11827310.9910.0490.1280.47799.9
2.34-2.436.50.10526980.9920.0450.1140.45999.9
2.43-2.546.10.09426950.9910.0420.1030.45399.9
2.54-2.676.80.08427320.9950.0350.0920.44799.9
2.67-2.846.70.07527110.9950.0310.0810.436100
2.84-3.066.70.06727340.9960.0280.0730.418100
3.06-3.376.20.05827640.9970.0250.0630.415100
3.37-3.866.80.05327530.9970.0220.0580.41299.9
3.86-4.866.20.04928030.9970.0210.0530.37999.8
4.86-506.20.04729710.9980.0210.0520.32499.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.79→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.19 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.102
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2062 2681 4.9 %RANDOM
Rwork0.1762 ---
obs0.1777 51687 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 136.32 Å2 / Biso mean: 25.729 Å2 / Biso min: 10.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å2-0 Å20 Å2
2--0.14 Å20 Å2
3----0.89 Å2
Refinement stepCycle: final / Resolution: 1.79→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3528 0 0 260 3788
Biso mean---25.79 -
Num. residues----450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193616
X-RAY DIFFRACTIONr_bond_other_d00.023431
X-RAY DIFFRACTIONr_angle_refined_deg1.2031.9444905
X-RAY DIFFRACTIONr_angle_other_deg0.67537853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5975449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91223.295173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.69415591
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2561529
X-RAY DIFFRACTIONr_chiral_restr0.0990.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0214142
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02883
LS refinement shellResolution: 1.791→1.838 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 195 -
Rwork0.21 3694 -
all-3889 -
obs--98.13 %
Refinement TLS params.Method: refined / Origin x: 15.5595 Å / Origin y: 30.9132 Å / Origin z: 62.1917 Å
111213212223313233
T0.0117 Å2-0.0069 Å20.0003 Å2-0.0053 Å20.0011 Å2--0.0054 Å2
L0.3226 °2-0.1898 °2-0.0872 °2-0.48 °20.1426 °2--0.3505 °2
S0.0231 Å °-0.021 Å °-0.0241 Å °0.0127 Å °-0.0126 Å °-0.0102 Å °-0.0041 Å °0.0148 Å °-0.0105 Å °

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