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- PDB-6ecw: StiD O-MT residues 956-1266 -

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Basic information

Entry
Database: PDB / ID: 6ecw
TitleStiD O-MT residues 956-1266
ComponentsStiD protein
KeywordsTRANSFERASE / methyltransferase
Function / homology
Function and homology information


DIM/DIP cell wall layer assembly / fatty acid synthase activity / secondary metabolite biosynthetic process / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / plasma membrane / cytoplasm
Similarity search - Function
: / Beta-ketoacyl synthase-like, N-terminal / Polyketide synthase, methyltransferase domain / Methyltransferase in polyketide synthase (PKS) enzymes. / Methyltransferase type 12 / Methyltransferase domain / PKS_PP_betabranch / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding ...: / Beta-ketoacyl synthase-like, N-terminal / Polyketide synthase, methyltransferase domain / Methyltransferase in polyketide synthase (PKS) enzymes. / Methyltransferase type 12 / Methyltransferase domain / PKS_PP_betabranch / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / PKS_KR / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Ketosynthase family 3 (KS3) domain profile. / 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-ADENOSYL-L-HOMOCYSTEINE / StiD protein
Similarity search - Component
Biological speciesStigmatella aurantiaca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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

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Assembly

Deposited unit
A: StiD protein
B: StiD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3424
Polymers70,5742
Non-polymers7692
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-6 kcal/mol
Surface area24410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.086, 71.086, 123.036
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein StiD protein


Mass: 35286.762 Da / Num. of mol.: 2 / Fragment: oxygen methyltransferase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stigmatella aurantiaca (bacteria) / Gene: stiD / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8RJY3
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.2 Å3/Da / Density % sol: 44.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.5 M ammonium citrate tribasic pH 7.2

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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: Aug 12, 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: 1.7→46.532 Å / Num. obs: 67485 / % possible obs: 99.9 % / Redundancy: 13.811 % / Biso Wilson estimate: 38.083 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.087 / Χ2: 1.103 / Net I/σ(I): 19.77 / Num. measured all: 932033
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.813.6662.0981.22108350.4782.17999.7
1.8-1.9213.4061.1422.38102420.7791.187100
1.92-2.0813.9890.5815.4695020.9480.603100
2.08-2.2714.1790.32110.7287910.9860.333100
2.27-2.5413.6010.18817.179440.9950.195100
2.54-2.9313.9650.09928.9869920.9980.103100
2.93-3.5914.5130.05549.6959620.9990.057100
3.59-5.0613.4090.03769.72461210.038100
5.06-46.53213.4430.03174.59260510.03299.7

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→46.532 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.62
RfactorNum. reflection% reflection
Rfree0.2114 1989 2.94 %
Rwork0.1686 --
obs0.1698 67382 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 135.25 Å2 / Biso mean: 48.0865 Å2 / Biso min: 19.04 Å2
Refinement stepCycle: final / Resolution: 1.7→46.532 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4465 0 52 312 4829
Biso mean--74.2 50.07 -
Num. residues----561
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6956-1.71630.34751410.32294476461798
1.7163-1.7380.36341460.311846544800100
1.738-1.76090.31081420.291945974739100
1.7609-1.7850.28321520.300347454897100
1.785-1.81050.37911300.332845394669100
1.8105-1.83750.3011440.3345694713100
1.8375-1.86620.31311400.302847174857100
1.8662-1.89680.26971460.2846494795100
1.8968-1.92950.29831400.24446054745100
1.9295-1.96460.23331360.220646094745100
1.9646-2.00240.25791420.193646224764100
2.0024-2.04330.20481380.184746584796100
2.0433-2.08770.21181440.183546404784100
2.0877-2.13630.19141400.180146164756100
2.1363-2.18970.22161410.175545994740100
2.1897-2.24890.20761400.168846094749100
2.2489-2.31510.19171400.168445904730100
2.3151-2.38980.2221400.163947214861100
2.3898-2.47520.2151420.178845964738100
2.4752-2.57430.24161340.173946344768100
2.5743-2.69150.21421460.173346424788100
2.6915-2.83330.23041420.173646364778100
2.8333-3.01080.22571350.171445944729100
3.0108-3.24320.23011440.165747274871100
3.2432-3.56950.21441380.154645774715100
3.5695-4.08580.13341280.131546144742100
4.0858-5.14660.18111420.120946394781100
5.1466-46.54940.18881360.152646184754100
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)
16.97093.38113.77383.10052.78733.10250.2307-0.8590.31180.0906-0.66750.71140.1409-1.3250.34820.2854-0.0862-0.02610.5756-0.07230.39398.2623-29.8472-0.6081
23.2117-0.7075-0.08884.0455-0.00092.2644-0.02050.32950.3457-0.7318-0.02960.8255-0.318-0.32640.08570.38330.0206-0.19850.29090.0640.413322.4034-13.253-5.7049
35.93412.29442.41491.44780.88491.8964-0.03610.2962-0.0106-0.0850.0630.19670.0526-0.0422-0.0440.20490.0088-0.02620.19930.0060.185722.7426-29.5101-4.7761
47.2153-3.2643.79973.153-2.84932.89940.19730.8120.3072-0.099-0.6222-0.74060.19771.15270.31410.2780.0929-0.01980.54630.05920.37662.8159-30.021617.8072
55.58231.67180.13612.47410.87884.68810.0636-0.25070.36120.41950.055-1.7324-0.26931.0005-0.0460.4389-0.0994-0.35740.3856-0.06770.929557.2478-8.908120.0474
62.85510.79750.21283.2607-0.08371.67920.0437-0.42990.23470.8806-0.1144-0.3478-0.2583-0.00550.08430.4086-0.0013-0.09640.2837-0.05480.244941.7859-16.911225.4481
75.674-2.26952.32331.616-0.81551.82260.0021-0.2747-0.01280.04420.045-0.19410.08250.0449-0.05160.2078-0.0123-0.01670.20870.00320.193348.5611-29.560722.0971
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 978 through 1028 )A978 - 1028
2X-RAY DIFFRACTION2chain 'A' and (resid 1029 through 1170 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1171 through 1266 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 979 through 1028 )B979 - 1028
5X-RAY DIFFRACTION5chain 'B' and (resid 1029 through 1090 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 1091 through 1170 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 1171 through 1266 )B0

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