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- PDB-5mpt: Structure of the citrinin polyketide synthase CMeT domain -

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Basic information

Entry
Database: PDB / ID: 5mpt
TitleStructure of the citrinin polyketide synthase CMeT domain
ComponentsCitrinin polyketide synthase
KeywordsTRANSFERASE / PKS / polyketide / natural product / domain deconstruction / citrinin / C-methylation / methyltransferase
Function / homology
Function and homology information


phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / methyltransferase activity / fatty acid biosynthetic process / methylation
Similarity search - Function
Methyltransferase, fungal type, helix-turn-helix domain / Helix-turn-helix domain / Fatty acyl-coenzyme A reductase, NAD-binding domain / Male sterility protein / Starter unit:ACP transacylase / Starter unit:ACP transacylase in aflatoxin biosynthesis / Methyltransferase type 12 / Methyltransferase domain / Polyketide synthase, dehydratase domain superfamily / Malonyl-CoA ACP transacylase, ACP-binding ...Methyltransferase, fungal type, helix-turn-helix domain / Helix-turn-helix domain / Fatty acyl-coenzyme A reductase, NAD-binding domain / Male sterility protein / Starter unit:ACP transacylase / Starter unit:ACP transacylase in aflatoxin biosynthesis / Methyltransferase type 12 / Methyltransferase domain / Polyketide synthase, dehydratase domain superfamily / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / 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 / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / 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
S-ADENOSYL-L-HOMOCYSTEINE / Citrinin polyketide synthase
Similarity search - Component
Biological speciesMonascus purpureus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.648 Å
AuthorsHerbst, D.A. / Storm, P.A. / Townsend, C.A. / Maier, T.
Funding support Switzerland, United States, 3items
OrganizationGrant numberCountry
Swiss National Science Foundation159696 Switzerland
Swiss National Science Foundation145023 Switzerland
National Institutes of HealthES001670 United States
CitationJournal: Cell Chem Biol / Year: 2017
Title: Functional and Structural Analysis of Programmed C-Methylation in the Biosynthesis of the Fungal Polyketide Citrinin.
Authors: Storm, P.A. / Herbst, D.A. / Maier, T. / Townsend, C.A.
History
DepositionDec 19, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Mar 29, 2017Group: Database references
Revision 1.3Jun 21, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end
Revision 1.4Jan 31, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5May 8, 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: Citrinin polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2684
Polymers46,7601
Non-polymers5093
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint7 kcal/mol
Surface area16220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.370, 98.370, 133.430
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Citrinin polyketide synthase / Non-reducing polyketide synthase citS


Mass: 46759.641 Da / Num. of mol.: 1 / Fragment: UNP Q65Z23 residues 1780-2182
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monascus purpureus (fungus) / Gene: pksCT / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q65Z23, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSignificant difference density for an unidentified ligand is observed in the active site

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.7355.01
22.4750.22
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
290.151vapor diffusion, sitting drop6.50.1 M BIS-TRIS pH 6.57, 25% (w/v) PEG MME 2K
290.152vapor diffusion, sitting drop0.1 M BIS-TRIS pH 6.21, 21.4% (w/v) PEG MME 2K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06DA10.99998
SYNCHROTRONSLS X06DA21.90747
SYNCHROTRONSLS X06DA30.97929
Detector
TypeIDDetectorDate
DECTRIS PILATUS 2M-F1PIXELAug 22, 2016
DECTRIS PILATUS 2M-F2PIXELSep 9, 2016
DECTRIS PILATUS 2M-F3PIXELSep 9, 2016
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
3SINGLE WAVELENGTHMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
10.999981
21.907471
30.979291
Reflection

Biso Wilson estimate: 35.937 Å2 / Entry-ID: 5MPT

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsDiffraction-IDNet I/σ(I)
1.648-71.8045745398.96.6440.9990.08110.61
2.05-71.8455925397.98.50.9980.084215.62
1.85-50.217618499.810.40.9990.135313.75
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.648-1.68966.6231.5961.370.76194.3
2.05-2.12.61.0291.380.711281.7
1.85-1.910.22.7421.120.571399.7

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.648→71.804 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 37.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2173 2009 3.5 %
Rwork0.1872 --
obs0.1883 57412 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.648→71.804 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3002 0 34 274 3310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093164
X-RAY DIFFRACTIONf_angle_d0.9754306
X-RAY DIFFRACTIONf_dihedral_angle_d14.2831931
X-RAY DIFFRACTIONf_chiral_restr0.054493
X-RAY DIFFRACTIONf_plane_restr0.007562
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6484-1.68960.46031340.45343754X-RAY DIFFRACTION94
1.6896-1.73530.40821440.39533945X-RAY DIFFRACTION99
1.7353-1.78640.34991440.35073991X-RAY DIFFRACTION99
1.7864-1.8440.40621440.33453958X-RAY DIFFRACTION99
1.844-1.90990.39091420.36783901X-RAY DIFFRACTION97
1.9099-1.98640.3361420.3013932X-RAY DIFFRACTION99
1.9864-2.07680.27771460.2294003X-RAY DIFFRACTION100
2.0768-2.18630.26221460.21074025X-RAY DIFFRACTION99
2.1863-2.32330.27721410.24073884X-RAY DIFFRACTION98
2.3233-2.50270.20571450.17494015X-RAY DIFFRACTION100
2.5027-2.75460.17951450.16113989X-RAY DIFFRACTION100
2.7546-3.15320.2331450.16993984X-RAY DIFFRACTION100
3.1532-3.97260.17491450.15944004X-RAY DIFFRACTION100
3.9726-71.87190.15231460.13084018X-RAY DIFFRACTION100
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)
10.0224-0.00380.02170.0924-0.07770.0514-0.09920.0060.15810.04910.0337-0.0318-0.015-0.01800.1911-0.0115-0.02470.1768-0.03020.2858-2.884745.760314.7493
20.02480.00110.00250.0027-0.0080.01550.0081-0.06030.1209-0.0249-0.05940.20770.0646-0.012400.2156-0.02930.0240.1992-0.03630.3427-29.257725.036313.6641
30.05070.0438-0.00010.0538-0.05080.0996-0.02070.07120.03740.1642-0.0731-0.01270.0692-0.0191-00.3192-0.0390.03720.2154-0.03990.2726-30.392410.812821.4816
40.04650.0213-0.04830.0143-0.01430.1304-0.14430.0208-0.0068-0.13680.01290.19190.0690.0114-0.00020.2229-0.0176-0.02290.1945-0.01130.2513-24.017121.88533.2527
50.01690.00490.0228-0.00060.00520.02030.1290.00410.1079-0.0424-0.06350.04790.01550.0017-00.19160.0011-0.00530.18880.01950.2353-6.848743.33189.2741
60.0985-0.0734-0.02850.0974-0.05050.10320.1220.2611-0.0175-0.1229-0.1344-0.089300.0573-0.02950.25440.03330.02170.2698-0.00180.12551.480537.78691.7237
70.20880.3378-0.18860.6133-0.22730.32890.07420.126-0.1851-0.0818-0.2462-0.11760.05470.04-0.36080.24870.12480.00380.2368-0.11480.09064.052928.77030.1576
80.0339-0.01470.03150.04340.0160.04020.0707-0.0371-0.1371-0.0048-0.0419-0.06170.01680.022800.19470.0035-0.02810.1840.03020.2020.110228.154615.381
90.05930.01140.07750.06310.12320.2753-0.0642-0.1044-0.17120.1638-0.09060.03-0.0192-0.0435-0.03610.2208-0.0265-0.0230.22160.0710.2828-12.619319.010916.7083
100.20910.08580.00940.13950.00710.10510.0866-0.15330.00930.1378-0.11880.006-0.03360.0202-0.10990.2658-0.0323-0.01230.237-0.01190.0424-4.343935.277422.0374
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1785 through 1812 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1813 through 1840 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1841 through 1898 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1899 through 1958 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1959 through 1978 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1979 through 2021 )
7X-RAY DIFFRACTION7chain 'A' and (resid 2022 through 2059 )
8X-RAY DIFFRACTION8chain 'A' and (resid 2060 through 2098 )
9X-RAY DIFFRACTION9chain 'A' and (resid 2099 through 2125 )
10X-RAY DIFFRACTION10chain 'A' and (resid 2126 through 2163 )

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