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- PDB-6ecx: StiE O-MT residues 942-1257 -

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Basic information

Entry
Database: PDB / ID: 6ecx
TitleStiE O-MT residues 942-1257
ComponentsStiE protein
KeywordsTRANSFERASE / methyltransferase
Function / homology
Function and homology information


phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
Polyketide synthase, methyltransferase domain / Methyltransferase in polyketide synthase (PKS) enzymes. / Methyltransferase type 12 / Methyltransferase domain / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Acyl transferase domain superfamily ...Polyketide synthase, methyltransferase domain / Methyltransferase in polyketide synthase (PKS) enzymes. / Methyltransferase type 12 / Methyltransferase domain / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / 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 / 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-ADENOSYLMETHIONINE / StiE protein
Similarity search - Component
Biological speciesStigmatella aurantiaca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsSkiba, M.A. / Bivins, M.B. / Smith, J.L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK042303 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA108874 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM008353 United States
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Structural Basis of Polyketide Synthase O-Methylation.
Authors: Skiba, M.A. / Bivins, M.M. / Schultz, J.R. / Bernard, S.M. / Fiers, W.D. / Dan, Q. / Kulkarni, S. / Wipf, P. / Gerwick, W.H. / Sherman, D.H. / Aldrich, C.C. / Smith, J.L.
History
DepositionAug 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 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

Downloads & links

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Assembly

Deposited unit
A: StiE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8096
Polymers36,0421
Non-polymers7675
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-3 kcal/mol
Surface area13520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.565, 88.565, 86.077
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1449-

HOH

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Components

#1: Protein StiE protein


Mass: 36042.336 Da / Num. of mol.: 1 / Fragment: oxygen methyltransferase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stigmatella aurantiaca (bacteria) / Gene: stiE / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8RJY2
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.34 Å3/Da / Density % sol: 47.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 8000, 0.1 M HEPES pH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 7, 2016
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.9→44.282 Å / Num. obs: 27564 / % possible obs: 99.9 % / Redundancy: 13.003 % / Biso Wilson estimate: 48.288 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.071 / Χ2: 1.046 / Net I/σ(I): 21.18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.9-2.0113.2191.9371.2843400.592.01599.6
2.01-2.1512.9831.0532.4641220.8271.096100
2.15-2.3313.2450.5125.138500.9510.533100
2.33-2.5513.0530.2948.7235460.9840.305100
2.55-2.8513.1160.15516.0532390.9950.162100
2.85-3.2813.0840.0753128800.9990.078100
3.28-4.0213.0230.0456.4924610.9990.041100
4.02-5.6612.3840.0374.28195110.031100
5.66-44.28211.7980.02778.8117110.02899.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.46 Å44.28 Å
Translation6.46 Å44.28 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASER2.6.0phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→44.282 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.93
RfactorNum. reflection% reflection
Rfree0.2222 1371 4.97 %
Rwork0.1831 --
obs0.185 27550 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 181.52 Å2 / Biso mean: 70.3258 Å2 / Biso min: 29.33 Å2
Refinement stepCycle: final / Resolution: 1.9→44.282 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2282 0 51 119 2452
Biso mean--71.41 61.63 -
Num. residues----283
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8999-1.93640.31721550.32772599275497
1.9364-1.9760.32131380.307427342872100
1.976-2.01890.31741530.29927352888100
2.0189-2.06590.34041370.279626922829100
2.0659-2.11760.30711360.272527382874100
2.1176-2.17480.32321450.242927162861100
2.1748-2.23880.25471470.213627252872100
2.2388-2.31110.23611400.220527182858100
2.3111-2.39370.22511440.203727232867100
2.3937-2.48950.23911350.200727342869100
2.4895-2.60280.22111380.190927192857100
2.6028-2.740.22181370.183327282865100
2.74-2.91160.23471330.178127312864100
2.9116-3.13640.22211480.18927192867100
3.1364-3.45190.20721590.174727102869100
3.4519-3.95110.23861390.160227262865100
3.9511-4.97690.17921240.138227342858100
4.9769-44.29450.19591510.184327182869100
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)
18.463-4.0652-4.62114.52460.66125.939-0.35551.4719-0.0262-1.26520.10910.10890.3723-0.90520.04220.8177-0.2691-0.00661.17090.01420.7887-3.3956-18.2164-26.5911
28.0847-1.3685-1.06714.7687-2.8596.3334-0.19771.575-1.2872-1.6062-0.2176-0.74071.14650.27070.45940.8879-0.16530.25980.7714-0.19680.74531.8063-26.7325-26.6544
31.88120.1025-0.74144.86932.32053.07830.05420.2984-0.3261-0.9146-0.10410.2332-0.1404-0.03850.00740.5194-0.0103-0.13210.28590.00140.4068-19.8711-29.3128-18.7155
44.6187-0.3886-1.92752.01150.47853.05180.45160.55110.3433-0.5995-0.1076-0.3393-0.88330.2596-0.30180.6625-0.10340.05060.39360.04350.4252-10.0659-12.5865-17.9539
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 948 through 989 )A948 - 989
2X-RAY DIFFRACTION2chain 'A' and (resid 990 through 1018 )A990 - 1018
3X-RAY DIFFRACTION3chain 'A' and (resid 1019 through 1120 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1121 through 1257 )A0

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