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- PDB-6ect: StiE O-MT residues 961-1257 -

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Basic information

Entry
Database: PDB / ID: 6ect
TitleStiE O-MT residues 961-1257
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: 1.42 Å
AuthorsSkiba, M.A. / Bivins, M.M. / 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)36,9842
Polymers36,5861
Non-polymers3981
Water5,675315
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13240 Å2
Unit cell
Length a, b, c (Å)90.866, 90.866, 84.910
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-1463-

HOH

21A-1650-

HOH

31A-1685-

HOH

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Components

#1: Protein StiE protein


Mass: 36585.941 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 2.4 Å3/Da / Density % sol: 48.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 10% PEG 3350, 0.1 M sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 8, 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: 1.42→40.637 Å / Num. obs: 67400 / % possible obs: 99 % / Redundancy: 24.346 % / Biso Wilson estimate: 25.822 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.065 / Χ2: 1.051 / Net I/σ(I): 29.87
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.42-1.521.8320.9693.2103590.870.99296
1.5-1.6126.0950.5276.76102000.9720.538100
1.61-1.7425.6290.29811.5594890.990.304100
1.74-1.926.0730.17619.9487440.9970.17999.9
1.9-2.1224.1810.134.7578100.9980.10298.2
2.12-2.4523.6310.07149.3570130.9990.07399.1
2.45-324.5290.05165.3860260.9990.052100
3-4.2322.4480.04278.89474510.043100
4.23-40.63722.590.03884.05278910.03999.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.96 Å40.64 Å
Translation1.96 Å40.64 Å

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASER2.6.0phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→40.637 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.13
RfactorNum. reflection% reflection
Rfree0.1853 2011 2.97 %
Rwork0.1673 --
obs0.1678 67271 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 116.7 Å2 / Biso mean: 31.0993 Å2 / Biso min: 10.25 Å2
Refinement stepCycle: final / Resolution: 1.42→40.637 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2264 0 27 315 2606
Biso mean--18.71 39.2 -
Num. residues----279
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4173-1.43530.33371160.30683916403285
1.4353-1.45420.28831560.26494502465898
1.4542-1.47410.23911390.235246284767100
1.4741-1.49510.21931320.228847154847100
1.4951-1.51750.2121250.201446574782100
1.5175-1.54120.19831670.189445894756100
1.5412-1.56640.24061450.18446414786100
1.5664-1.59340.17671460.184146154761100
1.5934-1.62240.21211310.183246364767100
1.6224-1.65360.17161410.169246344775100
1.6536-1.68740.16771320.167746314763100
1.6874-1.72410.19191470.1646294776100
1.7241-1.76420.16891480.163846194767100
1.7642-1.80830.20021390.170346424781100
1.8083-1.85720.16891390.165846444783100
1.8572-1.91180.20951540.18134546470099
1.9118-1.97350.21281460.21424576472298
1.9735-2.04410.19921300.168245974727100
2.0441-2.12590.20621520.168946274779100
2.1259-2.22270.16071430.156446504793100
2.2227-2.33980.15881410.18184559470098
2.3398-2.48640.19461380.164746064744100
2.4864-2.67840.2061350.161746474782100
2.6784-2.94780.19561450.16446254770100
2.9478-3.37420.16031310.158546584789100
3.3742-4.25040.17171380.143546334771100
4.2504-40.65320.17291360.157146444780100
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)
10.82450.2004-0.06261.99470.77021.15880.00870.0774-0.0345-0.035-0.01990.05120.0613-0.02880.01110.1470.0002-0.01570.11180.01160.137125.14315.62824.9578
23.0162-0.472-1.0481.04850.08331.71170.1490.32920.2217-0.1536-0.1062-0.2025-0.22360.072-0.09750.1741-0.00670.00180.12040.03910.175734.561832.394625.267
37.20092.3326-0.28586.38151.80676.48360.02630.82220.2664-0.5797-0.19490.18-0.0952-0.23330.15450.22530.05490.03520.26020.07170.172540.865223.563215.7476
44.31840.3803-1.20763.48740.32897.0696-0.09490.742-0.2936-0.7035-0.0406-0.4830.3990.49460.03150.27690.05830.07170.3085-0.00480.238345.747617.499615.3028
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1019 through 1134 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1135 through 1257 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid -9 through 989 )A-9 - 989
4X-RAY DIFFRACTION4chain 'A' and (resid 990 through 1018 )A990 - 1018

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