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

ID or keywords:

Entry

Database: PDB / ID: 3g5t

Title

Crystal structure of trans-aconitate 3-methyltransferase from yeast

Components

Trans-aconitate 3-methyltransferase

Keywords

TRANSFERASE /

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 /

methylation /

cytosol
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.119 Å

Authors

Burgie, E.S. / Bingman, C.A. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)

Citation

Journal: 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

Deposition	Feb 5, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 3, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3g5t.cif.gz	267 KB	Display	PDBx/mmCIF format
PDB format	pdb3g5t.ent.gz	226 KB	Display	PDB format
PDBx/mmJSON format	3g5t.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g5/3g5t ftp://data.pdbj.org/pub/pdb/validation_reports/g5/3g5t	HTTPS FTP

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Related structure data

Similar structure data	5eyd-d 5iug-d 6hzu-2 6mwe-1 6rse-2 5uab-d 6gla-2 3ccn-d 6tpe-1 5e1e-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: GO.93235

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Trans-aconitate 3-methyltransferase

hetero molecules

36.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

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 number	19
Space group name H-M	P2₁2₁2₁

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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

#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 / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine Type: L-peptide linking / 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 / 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 / Water Mass: 18.015 Da / Num. of mol.: 522 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.52 Å³/Da / Density % sol: 51.13 %
Crystal grow	Temperature: 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

Crystal

Density Matthews: 2.52 Å³/Da / Density % sol: 51.13 %

Crystal grow

Temperature: 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 ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-D / Wavelength: 0.97886 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 10, 2008

Radiation

Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97886 Å / Relative weight: 1

Reflection

Resolution: 1.119→50 Å / Num. obs: 134803 / % possible obs: 97.4 % / Redundancy: 12.5 % / R_merge(I) obs: 0.104 / Χ²: 2.104 / Net I/σ(I): 32.628

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	Χ²	% possible all
1.119-1.16	6.5	0.322	4.464	10548	1.181	77.3
1.16-1.21	8.3	0.316		13341	1.26	97.6
1.21-1.26	10	0.302		13651	1.361	99.7
1.26-1.33	11.9	0.287		13692	1.522	99.7
1.33-1.41	13.4	0.274		13696	1.627	100
1.41-1.52	14.4	0.233		13800	1.852	100
1.52-1.67	14.6	0.174		13795	2.141	100
1.67-1.92	14.7	0.138		13884	2.237	100
1.92-2.41	14.8	0.098		13994	3.05	100
2.41-50	14.3	0.075		14402	3.29	99.6

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Phasing

Phasing

Method:

SAD

Phasing MAD set

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

ID	R cullis acentric	Power acentric	Reflection acentric	Reflection centric
ISO_1	0	0	69672	6755
ANO_1	0.599	1.99	67549	0

Phasing MAD set shell

R cullis centric: 0 / Power centric: 0

ID	Resolution (Å)	R cullis acentric	Power acentric	Reflection acentric	Reflection centric
ISO_1	5.94-32.64	0	0	710	347
ISO_1	4.24-5.94	0	0	1377	349
ISO_1	3.47-4.24	0	0	1840	363
ISO_1	3.01-3.47	0	0	2202	359
ISO_1	2.69-3.01	0	0	2513	354
ISO_1	2.46-2.69	0	0	2777	360
ISO_1	2.28-2.46	0	0	3073	365
ISO_1	2.13-2.28	0	0	3297	364
ISO_1	2.01-2.13	0	0	3513	358
ISO_1	1.91-2.01	0	0	3713	349
ISO_1	1.82-1.91	0	0	3933	366
ISO_1	1.74-1.82	0	0	4085	345
ISO_1	1.67-1.74	0	0	4273	360
ISO_1	1.61-1.67	0	0	4443	346
ISO_1	1.56-1.61	0	0	4626	347
ISO_1	1.51-1.56	0	0	4711	335
ISO_1	1.46-1.51	0	0	4737	315
ISO_1	1.42-1.46	0	0	4698	262
ISO_1	1.39-1.42	0	0	4703	268
ISO_1	1.35-1.39	0	0	4448	243
ANO_1	5.94-32.64	0.409	3	709	0
ANO_1	4.24-5.94	0.43	2.752	1377	0
ANO_1	3.47-4.24	0.48	2.667	1840	0
ANO_1	3.01-3.47	0.464	2.914	2202	0
ANO_1	2.69-3.01	0.423	3.102	2513	0
ANO_1	2.46-2.69	0.423	3.19	2777	0
ANO_1	2.28-2.46	0.45	3.087	3073	0
ANO_1	2.13-2.28	0.459	2.886	3297	0
ANO_1	2.01-2.13	0.493	2.673	3513	0
ANO_1	1.91-2.01	0.523	2.432	3709	0
ANO_1	1.82-1.91	0.554	2.221	3925	0
ANO_1	1.74-1.82	0.611	1.931	4079	0
ANO_1	1.67-1.74	0.649	1.742	4237	0
ANO_1	1.61-1.67	0.683	1.605	4361	0
ANO_1	1.56-1.61	0.71	1.505	4487	0
ANO_1	1.51-1.56	0.746	1.337	4580	0
ANO_1	1.46-1.51	0.797	1.208	4539	0
ANO_1	1.42-1.46	0.877	0.928	4383	0
ANO_1	1.39-1.42	0.871	0.989	4192	0
ANO_1	1.35-1.39	0.907	0.916	3756	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	-5.481	-86.919	-6.032	SE	8.97	1.73
2	-6.724	-86.716	-10.897	SE	10.87	1.33
3	-6.467	-5.149	-43.014	SE	11.86	1.17
4	-8.049	-79.582	-54.332	SE	9.32	0.92
5	-3.112	-4.127	-12.842	SE	9.3	0.73
6	-4.775	-15.199	-93.643	SE	12.81	0.5

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 57708

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
7.59-100	72.2	0.822	515
5.55-7.59	62.5	0.886	768
4.58-5.55	55.2	0.931	934
3.99-4.58	58.6	0.92	1092
3.58-3.99	58.4	0.911	1217
3.28-3.58	58.4	0.899	1326
3.04-3.28	61.3	0.893	1451
2.85-3.04	57.1	0.894	1530
2.69-2.85	56.1	0.91	1629
2.55-2.69	56.1	0.912	1724
2.44-2.55	57.2	0.906	1778
2.33-2.44	56.2	0.903	1875
2.24-2.33	57.5	0.912	1959
2.16-2.24	57.6	0.903	2009
2.09-2.16	56.6	0.902	2089
2.02-2.09	58.3	0.905	2135
1.96-2.02	59.1	0.901	2238
1.91-1.96	58.1	0.902	2270
1.86-1.91	59.4	0.904	2336
1.81-1.86	58.1	0.894	2401
1.77-1.81	57.9	0.898	2419
1.73-1.77	59.1	0.885	2558
1.69-1.73	61.5	0.893	2529
1.65-1.69	61.1	0.892	2613
1.62-1.65	61.4	0.881	2642
1.59-1.62	63.5	0.877	2690
1.56-1.59	64.7	0.864	2750
1.53-1.56	66.2	0.845	2750
1.5-1.53	67.2	0.783	3481

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
DM	5	phasing
REFMAC	5.5.0066	refinement
PDB_EXTRACT	3.006	data extraction
Blu-Ice		data collection
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 1.119→34.47 Å / Cor.coef. F_o:F_c: 0.977 / Cor.coef. F_o:F_c free: 0.972 / Matrix type: sparse / WR_factor R_free: 0.139 / WR_factor R_work: 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.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.137	6751	5.019 %	RANDOM
R_work	0.12	127751	-	-
obs	0.121	134502	98.176 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK

Displacement parameters

B_iso max: 54.9 Å² / B_iso mean: 12.564 Å² / B_iso min: 4.71 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.161 Å²	0 Å²	0 Å²
2-	-	0.02 Å²	0 Å²
3-	-	-	0.142 Å²

Refinement step

Cycle: LAST / Resolution: 1.119→34.47 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4891	0	75	541	5507

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.03	0.022	2767
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2264
X-RAY DIFFRACTION	r_angle_refined_deg	2.262	1.979	3710
X-RAY DIFFRACTION	r_angle_other_deg	0.88	3	5296
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.074	5	311
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.672	24.476	143
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.732	15	543
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.26	15	17
X-RAY DIFFRACTION	r_chiral_restr	0.154	0.2	372
X-RAY DIFFRACTION	r_gen_planes_refined	0.013	0.021	2958
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	548
X-RAY DIFFRACTION	r_mcbond_it	2.263	1.5	1546
X-RAY DIFFRACTION	r_mcbond_other	1.103	1.5	601
X-RAY DIFFRACTION	r_mcangle_it	3.212	2	2554
X-RAY DIFFRACTION	r_scbond_it	4.455	3	1221
X-RAY DIFFRACTION	r_scangle_it	5.801	4.5	1155
X-RAY DIFFRACTION	r_rigid_bond_restr	2.402	3	5031
X-RAY DIFFRACTION	r_sphericity_free	15.644	3	541
X-RAY DIFFRACTION	r_sphericity_bonded	6.338	3	4966

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	% reflection obs (%)	WR_factor R_work
1.119-1.148	0.158	439	0.146	7901	0.147	10029	83.159	0.115
1.148-1.18	0.143	433	0.121	8936	0.122	9748	96.112	0.096
1.18-1.214	0.129	448	0.109	8928	0.11	9471	98.997	0.087
1.214-1.251	0.122	487	0.103	8709	0.104	9250	99.416	0.085
1.251-1.292	0.117	478	0.096	8437	0.097	8953	99.576	0.08
1.292-1.338	0.119	423	0.093	8230	0.094	8690	99.574	0.078
1.338-1.388	0.121	436	0.092	7908	0.093	8381	99.559	0.081
1.388-1.445	0.111	371	0.092	7649	0.093	8060	99.504	0.082
1.445-1.509	0.101	386	0.089	7362	0.09	7782	99.563	0.083
1.509-1.583	0.114	390	0.089	7017	0.091	7425	99.758	0.085
1.583-1.668	0.118	372	0.092	6680	0.093	7067	99.788	0.089
1.668-1.769	0.113	325	0.097	6376	0.098	6708	99.896	0.1
1.769-1.891	0.119	300	0.106	6003	0.106	6307	99.937	0.113
1.891-2.043	0.123	296	0.107	5627	0.108	5925	99.966	0.117
2.043-2.238	0.131	263	0.112	5155	0.113	5418	100	0.127
2.238-2.501	0.137	263	0.123	4688	0.123	4951	100	0.145
2.501-2.888	0.142	232	0.136	4160	0.136	4392	100	0.164
2.888-3.535	0.168	205	0.143	3538	0.144	3744	99.973	0.181
3.535-4.993	0.144	124	0.142	2828	0.142	2957	99.831	0.195
4.993-34.47	0.264	80	0.268	1619	0.268	1743	97.476	0.367

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