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- PDB-5thz: Crystal structure of CurJ carbon methyltransferase -

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Basic information

Entry
Database: PDB / ID: 5thz
TitleCrystal structure of 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 / : / Methyltransferase type 12 / Methyltransferase domain / : / Polyketide synthase dehydratase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. ...Helix-turn-helix domain / : / Beta-ketoacyl synthase-like, N-terminal / : / Methyltransferase type 12 / Methyltransferase domain / : / Polyketide synthase dehydratase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / 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
CITRATE ANION / S-ADENOSYL-L-HOMOCYSTEINE / CurJ
Similarity search - Component
Biological speciesMoorea producens 3L (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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 1.4Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
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
B: CurJ
A: CurJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,4066
Polymers90,3562
Non-polymers1,0504
Water2,900161
1
B: CurJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6543
Polymers45,1781
Non-polymers4772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: CurJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7513
Polymers45,1781
Non-polymers5742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.124, 129.131, 63.076
Angle α, β, γ (deg.)90.000, 111.460, 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: 45177.980 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


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 39.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.30 M NaCitrate, 2 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: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 21, 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: 2.08→43.442 Å / Num. obs: 39931 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 36.01 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.151 / Net I/σ(I): 9.15
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.08-2.211.0511.270.684193.6
2.21-2.360.8491.970.94199.8
2.36-2.550.5743.040.922199.9
2.55-2.790.4224.550.952199.7
2.79-3.120.2577.930.981199.8
3.12-3.60.14514.740.993199.9
3.6-4.40.08922.410.996199.6
4.4-6.190.06726.920.997199.7
6.19-43.4420.04932.670.998198.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.98 Å43.43 Å
Translation1.98 Å43.43 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
XSCALEdata scaling
PHASER2.6.0phasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5THY

5thy


Resolution: 2.1→43.435 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.76
RfactorNum. reflection% reflection
Rfree0.2516 3358 4.27 %
Rwork0.1853 --
obs0.1881 39893 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 140.68 Å2 / Biso mean: 51.9024 Å2 / Biso min: 17.8 Å2
Refinement stepCycle: final / Resolution: 2.1→43.435 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5988 0 71 161 6220
Biso mean--51.63 44.5 -
Num. residues----763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076176
X-RAY DIFFRACTIONf_angle_d0.9198418
X-RAY DIFFRACTIONf_chiral_restr0.05990
X-RAY DIFFRACTIONf_plane_restr0.0071076
X-RAY DIFFRACTIONf_dihedral_angle_d17.0443719
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.130.381400.311330043144100
2.13-2.16180.34841370.30231673304100
2.1618-2.19560.35531440.307531733317100
2.1956-2.23160.38311360.33193110324699
2.2316-2.27010.39331360.34053091322798
2.2701-2.31130.3581380.31243155329399
2.3113-2.35580.35561450.28473075322099
2.3558-2.40390.33911390.273431703309100
2.4039-2.45610.2871420.248730933235100
2.4561-2.51330.2721410.236632023343100
2.5133-2.57610.34381460.239731223268100
2.5761-2.64570.30711330.251531643297100
2.6457-2.72360.34541410.24093163330499
2.7236-2.81150.38121360.2431093245100
2.8115-2.9120.27751340.215831823316100
2.912-3.02850.28571440.19931243268100
3.0285-3.16630.30871440.182531613305100
3.1663-3.33320.21651400.164831713311100
3.3332-3.54190.2591360.149831573293100
3.5419-3.81530.18911410.138631393280100
3.8153-4.19890.19151400.132131753315100
4.1989-4.80580.18941440.115431183262100
4.8058-6.05220.20041410.147131243265100
6.0522-43.44410.16991400.143145328599
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)
16.55863.0291-3.84932.3767-1.90264.3540.3365-0.45160.0770.3097-0.12730.1162-0.1640.3052-0.1910.69330.0202-0.06640.302-0.02770.3448-6.712818.58236.3195
27.09371.92812.68423.69871.6262.32770.317-0.29410.14120.1631-0.1963-0.19450.2421-0.20480.02340.7092-0.07530.09180.32150.01250.328-0.9978.8879-31.0698
34.21920.8156-0.38472.0554-0.6946.99210.08390.67060.3199-0.30760.20060.1947-0.3622-1.255-0.1230.77020.0767-0.01770.60440.07680.317-16.893310.3469-40.2317
43.60280.07670.40651.3315-0.1465.78350.1822-0.0181-0.1087-0.1467-0.1435-0.10970.37140.0389-0.04540.69090.01590.02620.2372-0.00230.2802-2.50061.3491-30.2698
50.4847-0.4168-0.30073.40120.60281.6156-0.04290.0432-0.1503-0.17880.0471-0.18720.97110.1268-0.19250.6065-0.0329-0.01170.34160.00670.2922-3.3935.6562-8.3169
62.3305-0.04620.05132.6741-0.08962.9385-0.0029-0.1411-0.0590.36760.0068-0.03450.07080.0593-0.02340.3053-0.0165-0.00630.1462-0.00020.192-15.0264.4989-0.1327
72.00280.2852-0.36852.43920.86914.0562-0.00220.23190.2534-0.37540.1053-0.0036-0.37870.0402-0.05280.5469-0.0312-0.01720.2230.0380.2717-13.973216.8162-14.8801
87.9543-1.83853.51764.558-2.50117.62850.2066-0.4133-0.87760.37020.37160.63940.3024-0.607-0.50890.6029-0.00780.10140.21220.00960.45881.1875-31.4826-0.5068
93.8705-0.8056-1.68782.30641.38235.9166-0.03620.5257-0.149-0.41870.01760.1087-0.37320.02260.0120.6991-0.0618-0.07890.386-0.00920.30438.0549-15.893-32.28
101.8885-0.11-1.39191.9247-1.62585.07380.1666-0.51920.02150.9206-0.04520.3050.07650.007-0.09770.52940.01130.06960.25410.00050.35537.3604-20.25032.3579
113.74770.064-0.61693.80260.1743.36740.0607-0.16290.16190.2589-0.00370.0997-0.1112-0.0325-0.04310.2392-0.015-0.01860.13360.02510.185115.9456-14.2142-1.4655
122.32870.5659-0.12112.512-2.32057.251-0.10260.2699-0.4219-0.36440.20870.05250.4365-0.0248-0.11490.483-0.0121-0.00180.1891-0.0530.296514.2903-27.1312-14.8931
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid -5 through 28 )B-5 - 28
2X-RAY DIFFRACTION2chain 'B' and (resid 29 through 54 )B29 - 54
3X-RAY DIFFRACTION3chain 'B' and (resid 55 through 105 )B55 - 105
4X-RAY DIFFRACTION4chain 'B' and (resid 106 through 156 )B106 - 156
5X-RAY DIFFRACTION5chain 'B' and (resid 157 through 189 )B157 - 189
6X-RAY DIFFRACTION6chain 'B' and (resid 190 through 307 )B190 - 307
7X-RAY DIFFRACTION7chain 'B' and (resid 308 through 381 )B308 - 381
8X-RAY DIFFRACTION8chain 'A' and (resid 6 through 28 )A6 - 28
9X-RAY DIFFRACTION9chain 'A' and (resid 29 through 172 )A29 - 172
10X-RAY DIFFRACTION10chain 'A' and (resid 173 through 211 )A173 - 211
11X-RAY DIFFRACTION11chain 'A' and (resid 212 through 307 )A212 - 307
12X-RAY DIFFRACTION12chain 'A' and (resid 308 through 381 )A308 - 381

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