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- PDB-5thy: Crystal structure of SeMet-Substituted CurJ carbon methyltransferase -

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Basic information

Entry
Database: PDB / ID: 5thy
TitleCrystal structure of SeMet-Substituted CurJ carbon methyltransferase
ComponentsCurJ
KeywordsTRANSFERASE / LYASE / 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
Helix-turn-helix domain / : / Beta-ketoacyl synthase-like, N-terminal / : / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Methyltransferase type 12 / Methyltransferase domain / : / Polyketide synthase dehydratase domain ...Helix-turn-helix domain / : / Beta-ketoacyl synthase-like, N-terminal / : / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Methyltransferase type 12 / Methyltransferase domain / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / 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
OXIDIZED GLUTATHIONE DISULFIDE / S-ADENOSYL-L-HOMOCYSTEINE / CurJ
Similarity search - Component
Biological speciesMoorea producens 3L (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.087 Å
AuthorsSkiba, M.A. / 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)T32GM008353 United States
CitationJournal: ACS Chem. Biol. / Year: 2016
Title: Domain Organization and Active Site Architecture of a Polyketide Synthase C-methyltransferase.
Authors: Skiba, M.A. / Sikkema, A.P. / Fiers, W.D. / Gerwick, W.H. / Sherman, D.H. / Aldrich, C.C. / Smith, J.L.
History
DepositionSep 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references
Revision 1.2Dec 28, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.5Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.6Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CurJ
B: CurJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,3005
Polymers90,9192
Non-polymers1,3813
Water4,792266
1
A: CurJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8442
Polymers45,4591
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CurJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4563
Polymers45,4591
Non-polymers9972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.350, 130.390, 62.830
Angle α, β, γ (deg.)90.000, 111.980, 90.000
Int Tables number4
Space group name H-MP1211
DetailsMonomer as determined by gel filtration

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Components

#1: Protein CurJ / Polyketide synthase module


Mass: 45459.348 Da / Num. of mol.: 2 / Fragment: residues 1269-1649
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moorea producens 3L (bacteria) / Gene: LYNGBM3L_74460 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F4Y426
#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: Chemical ChemComp-GDS / OXIDIZED GLUTATHIONE DISULFIDE / Glutathione disulfide


Mass: 612.631 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H32N6O12S2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.02 Å3/Da / Density % sol: 39.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.37 M NaCitrate, 1 mM GSH/GSSG, 5% Acetone

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 11, 2015
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.087→44.84 Å / Num. obs: 84469 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 10.8 % / Biso Wilson estimate: 37.69 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.163 / Net I/σ(I): 8.25
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.09-2.141.51.660.409199.6
2.14-2.21.2682.30.529199.4
2.2-2.261.0942.670.6051100
2.26-2.330.9813.040.659199.3
2.33-2.410.8573.610.761199.7
2.41-2.490.7324.240.8311100
2.49-2.590.6544.630.854199.3
2.59-2.690.5315.310.893199.7
2.69-2.810.4376.40.9181100
2.81-2.950.3487.60.956199.4
2.95-3.110.289.220.967199.8
3.11-3.30.19911.70.9831100
3.3-3.530.16113.510.985199.7
3.53-3.810.1415.830.991199.7
3.81-4.170.10318.790.994199.7
4.17-4.670.08220.260.994199.5
4.67-5.390.07619.690.994199.1
5.39-6.60.08219.420.995199.9
6.6-9.330.06122.780.997198.7
9.330.05325.740.995196.3

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XSCALEdata scaling
SHELXphasing
RESOLVEphasing
PHENIX(1.10_2155)refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.087→44.836 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.34
RfactorNum. reflection% reflection
Rfree0.2155 4476 5.3 %
Rwork0.1685 --
obs0.171 84408 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 145.91 Å2 / Biso mean: 46.3138 Å2 / Biso min: 21.07 Å2
Refinement stepCycle: final / Resolution: 2.087→44.836 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5988 0 92 266 6346
Biso mean--69.86 46.81 -
Num. residues----763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036208
X-RAY DIFFRACTIONf_angle_d0.5988462
X-RAY DIFFRACTIONf_chiral_restr0.043995
X-RAY DIFFRACTIONf_plane_restr0.0041085
X-RAY DIFFRACTIONf_dihedral_angle_d11.6733740
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.087-2.11070.33651480.33222658280697
2.1107-2.13560.28411420.268125962738100
2.1356-2.16160.3021610.246426782839100
2.1616-2.1890.29331390.245726812820100
2.189-2.21780.30171560.247826522808100
2.2178-2.24820.29851450.23626642809100
2.2482-2.28030.27891640.227826682832100
2.2803-2.31430.29981420.222126782820100
2.3143-2.35050.30881520.223826462798100
2.3505-2.3890.30391520.226426452797100
2.389-2.43020.24851480.219627312879100
2.4302-2.47440.2611520.210625812733100
2.4744-2.5220.2531490.209727432892100
2.522-2.57340.28681550.206526252780100
2.5734-2.62940.25231460.206226902836100
2.6294-2.69060.24191520.193826482800100
2.6906-2.75780.25711540.190826512805100
2.7578-2.83240.31411560.195826952851100
2.8324-2.91570.27591330.226472780100
2.9157-3.00980.2551590.194727262885100
3.0098-3.11740.23481460.18126202766100
3.1174-3.24210.21371350.163226812816100
3.2421-3.38960.20921490.149726552804100
3.3896-3.56830.21380.146326722810100
3.5683-3.79170.171480.13526782826100
3.7917-4.08430.17991550.124326872842100
4.0843-4.4950.151440.114526822826100
4.495-5.14460.1721570.128126442801100
5.1446-6.47860.22651490.163926672816100
6.4786-44.84630.13941500.14432643279399
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)
10.5795-0.1967-0.01233.3886-3.79144.3115-0.01010.19290.25490.1550.10050.173-0.3922-0.3516-0.26780.32570.05150.08550.40050.00490.3901-25.292888.188422.7074
21.216-0.03120.55090.9106-0.21653.02780.0744-0.1463-0.00480.0903-0.02380.0321-0.03480.0225-0.04730.22140.00770.03690.2597-0.01430.2754-15.218280.979229.4805
31.3672-0.2129-0.32081.44790.12893.66470.00780.0574-0.0686-0.1541-0.00160.09210.0761-0.1132-0.00930.23970.012-0.00390.21290.00350.3042-8.303481.02493.7952
43.6999-1.20450.83423.9773-1.936.280.0368-0.25020.40290.12220.05170.18-0.5897-0.3435-0.06530.28580.02060.02830.2183-0.04420.3425-10.029994.722110.2619
55.0516-6.3806-5.33988.06076.74425.642-0.113-0.1536-0.27790.08740.0699-0.17950.54170.3699-0.03130.32310.0504-0.06630.4128-0.0060.361322.296655.498630.6247
61.2808-0.1295-0.65351.44130.31073.29450.0184-0.1511-0.06530.08230.0151-0.07440.110.0399-0.01590.20670.0003-0.04030.22720.02440.305214.298658.930826.4533
71.6393-0.28160.06771.1718-0.15193.19140.04730.1008-0.0174-0.06870.005-0.0033-0.11010.0127-0.06020.20940.0186-0.00890.1655-0.02550.26887.428359.82925.2836
84.03-1.3179-2.40773.64233.30457.6076-0.1419-0.259-0.40890.3340.0747-0.02910.67250.29490.060.39950.0158-0.0350.20690.05360.38719.545545.519810.5448
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 52 )A19 - 52
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 186 )A53 - 186
3X-RAY DIFFRACTION3chain 'A' and (resid 187 through 331 )A187 - 331
4X-RAY DIFFRACTION4chain 'A' and (resid 332 through 381 )A332 - 381
5X-RAY DIFFRACTION5chain 'B' and (resid 30 through 52 )B30 - 52
6X-RAY DIFFRACTION6chain 'B' and (resid 53 through 196 )B53 - 196
7X-RAY DIFFRACTION7chain 'B' and (resid 197 through 331 )B197 - 331
8X-RAY DIFFRACTION8chain 'B' and (resid 332 through 381 )B332 - 381

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