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- PDB-3g5t: Crystal structure of trans-aconitate 3-methyltransferase from yeast -

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Basic information

Entry
Database: PDB / ID: 3g5t
TitleCrystal structure of trans-aconitate 3-methyltransferase from yeast
ComponentsTrans-aconitate 3-methyltransferase
KeywordsTRANSFERASE / Methyltransferase / Structural Genomics / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG / Cytoplasm / Phosphoprotein / S-adenosyl-L-methionine
Function / homology
Function and homology information


trans-aconitate 3-methyltransferase / trans-aconitate 3-methyltransferase activity / cellular response to amino acid starvation / methylation / cytosol
Similarity search - Function
: / Methyltransferase domain / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / (2E)-2-(2-methoxy-2-oxoethyl)but-2-enedioic acid / Trans-aconitate 3-methyltransferase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.119 Å
AuthorsBurgie, E.S. / Bingman, C.A. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: To be Published
Title: Crystal structure of trans-aconitate 3-methyltransferase from yeast
Authors: Burgie, E.S. / Bingman, C.A. / Wesenberg, G.E. / Phillips Jr., G.N.
History
DepositionFeb 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trans-aconitate 3-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,20212
Polymers35,0551
Non-polymers1,14711
Water9,404522
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.834, 91.891, 104.269
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Trans-aconitate 3-methyltransferase


Mass: 35054.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: P32643, S000000977, SYGP-ORF63, TAM1, TMT1, YER175C / Plasmid: pVP68K / Production host: Escherichia coli (E. coli) / Strain (production host): B834 p(RARE2)
References: UniProt: P32643, trans-aconitate 3-methyltransferase

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Non-polymers , 5 types, 533 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-T8N / (2E)-2-(2-methoxy-2-oxoethyl)but-2-enedioic acid


Mass: 188.135 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8O6
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 522 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 51.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: Protein solution (8 mg/ml MSE Protein, 0.040 M NaCl, 0.00024 M TCEP, 0.001 M SAM, 0.008 M Trans-aconitic acid, 0.0045 M HEPES pH 7.0) mixed in a 1:1 ratio with the Well solution (24% PEG ...Details: Protein solution (8 mg/ml MSE Protein, 0.040 M NaCl, 0.00024 M TCEP, 0.001 M SAM, 0.008 M Trans-aconitic acid, 0.0045 M HEPES pH 7.0) mixed in a 1:1 ratio with the Well solution (24% PEG 8000, 2% DMSO, 0.05 M HEPES pH 7.5). Cryoprotected with 23% PEG 8000, 2% DMSO, 0.001 M SAM, 0.0085 M Trans-aconitate, 0.05 M HEPES pH 7.5, 19% Ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97886 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 10, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97886 Å / Relative weight: 1
ReflectionResolution: 1.119→50 Å / Num. obs: 134803 / % possible obs: 97.4 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.104 / Χ2: 2.104 / Net I/σ(I): 32.628
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.119-1.166.50.3224.464105481.18177.3
1.16-1.218.30.316133411.2697.6
1.21-1.26100.302136511.36199.7
1.26-1.3311.90.287136921.52299.7
1.33-1.4113.40.274136961.627100
1.41-1.5214.40.233138001.852100
1.52-1.6714.60.174137952.141100
1.67-1.9214.70.138138842.237100
1.92-2.4114.80.098139943.05100
2.41-5014.30.075144023.2999.6

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Phasing

PhasingMethod: SAD
Phasing MAD set

R cullis centric: 0 / Highest resolution: 1.35 Å / Lowest resolution: 32.64 Å / Power centric: 0

IDR cullis acentricPower acentricReflection acentricReflection centric
ISO_100696726755
ANO_10.5991.99675490
Phasing MAD set shell

R cullis centric: 0 / Power centric: 0

IDResolution (Å)R cullis acentricPower acentricReflection acentricReflection centric
ISO_15.94-32.6400710347
ISO_14.24-5.94001377349
ISO_13.47-4.24001840363
ISO_13.01-3.47002202359
ISO_12.69-3.01002513354
ISO_12.46-2.69002777360
ISO_12.28-2.46003073365
ISO_12.13-2.28003297364
ISO_12.01-2.13003513358
ISO_11.91-2.01003713349
ISO_11.82-1.91003933366
ISO_11.74-1.82004085345
ISO_11.67-1.74004273360
ISO_11.61-1.67004443346
ISO_11.56-1.61004626347
ISO_11.51-1.56004711335
ISO_11.46-1.51004737315
ISO_11.42-1.46004698262
ISO_11.39-1.42004703268
ISO_11.35-1.39004448243
ANO_15.94-32.640.40937090
ANO_14.24-5.940.432.75213770
ANO_13.47-4.240.482.66718400
ANO_13.01-3.470.4642.91422020
ANO_12.69-3.010.4233.10225130
ANO_12.46-2.690.4233.1927770
ANO_12.28-2.460.453.08730730
ANO_12.13-2.280.4592.88632970
ANO_12.01-2.130.4932.67335130
ANO_11.91-2.010.5232.43237090
ANO_11.82-1.910.5542.22139250
ANO_11.74-1.820.6111.93140790
ANO_11.67-1.740.6491.74242370
ANO_11.61-1.670.6831.60543610
ANO_11.56-1.610.711.50544870
ANO_11.51-1.560.7461.33745800
ANO_11.46-1.510.7971.20845390
ANO_11.42-1.460.8770.92843830
ANO_11.39-1.420.8710.98941920
ANO_11.35-1.390.9070.91637560
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
1-5.481-86.919-6.032SE8.971.73
2-6.724-86.716-10.897SE10.871.33
3-6.467-5.149-43.014SE11.861.17
4-8.049-79.582-54.332SE9.320.92
5-3.112-4.127-12.842SE9.30.73
6-4.775-15.199-93.643SE12.810.5
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 57708
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.59-10072.20.822515
5.55-7.5962.50.886768
4.58-5.5555.20.931934
3.99-4.5858.60.921092
3.58-3.9958.40.9111217
3.28-3.5858.40.8991326
3.04-3.2861.30.8931451
2.85-3.0457.10.8941530
2.69-2.8556.10.911629
2.55-2.6956.10.9121724
2.44-2.5557.20.9061778
2.33-2.4456.20.9031875
2.24-2.3357.50.9121959
2.16-2.2457.60.9032009
2.09-2.1656.60.9022089
2.02-2.0958.30.9052135
1.96-2.0259.10.9012238
1.91-1.9658.10.9022270
1.86-1.9159.40.9042336
1.81-1.8658.10.8942401
1.77-1.8157.90.8982419
1.73-1.7759.10.8852558
1.69-1.7361.50.8932529
1.65-1.6961.10.8922613
1.62-1.6561.40.8812642
1.59-1.6263.50.8772690
1.56-1.5964.70.8642750
1.53-1.5666.20.8452750
1.5-1.5367.20.7833481

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DM5phasing
REFMAC5.5.0066refinement
PDB_EXTRACT3.006data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.119→34.47 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.972 / Matrix type: sparse / WRfactor Rfree: 0.139 / WRfactor Rwork: 0.122 / Occupancy max: 1 / Occupancy min: 0.1 / SU B: 0 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.025 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.137 6751 5.019 %RANDOM
Rwork0.12 127751 --
obs0.121 134502 98.176 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso max: 54.9 Å2 / Biso mean: 12.564 Å2 / Biso min: 4.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.161 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0.142 Å2
Refinement stepCycle: LAST / Resolution: 1.119→34.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4891 0 75 541 5507
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0222767
X-RAY DIFFRACTIONr_bond_other_d0.0010.022264
X-RAY DIFFRACTIONr_angle_refined_deg2.2621.9793710
X-RAY DIFFRACTIONr_angle_other_deg0.8835296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0745311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.67224.476143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.73215543
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.261517
X-RAY DIFFRACTIONr_chiral_restr0.1540.2372
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212958
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02548
X-RAY DIFFRACTIONr_mcbond_it2.2631.51546
X-RAY DIFFRACTIONr_mcbond_other1.1031.5601
X-RAY DIFFRACTIONr_mcangle_it3.21222554
X-RAY DIFFRACTIONr_scbond_it4.45531221
X-RAY DIFFRACTIONr_scangle_it5.8014.51155
X-RAY DIFFRACTIONr_rigid_bond_restr2.40235031
X-RAY DIFFRACTIONr_sphericity_free15.6443541
X-RAY DIFFRACTIONr_sphericity_bonded6.33834966
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)WRfactor Rwork
1.119-1.1480.1584390.14679010.1471002983.1590.115
1.148-1.180.1434330.12189360.122974896.1120.096
1.18-1.2140.1294480.10989280.11947198.9970.087
1.214-1.2510.1224870.10387090.104925099.4160.085
1.251-1.2920.1174780.09684370.097895399.5760.08
1.292-1.3380.1194230.09382300.094869099.5740.078
1.338-1.3880.1214360.09279080.093838199.5590.081
1.388-1.4450.1113710.09276490.093806099.5040.082
1.445-1.5090.1013860.08973620.09778299.5630.083
1.509-1.5830.1143900.08970170.091742599.7580.085
1.583-1.6680.1183720.09266800.093706799.7880.089
1.668-1.7690.1133250.09763760.098670899.8960.1
1.769-1.8910.1193000.10660030.106630799.9370.113
1.891-2.0430.1232960.10756270.108592599.9660.117
2.043-2.2380.1312630.11251550.11354181000.127
2.238-2.5010.1372630.12346880.12349511000.145
2.501-2.8880.1422320.13641600.13643921000.164
2.888-3.5350.1682050.14335380.144374499.9730.181
3.535-4.9930.1441240.14228280.142295799.8310.195
4.993-34.470.264800.26816190.268174397.4760.367

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