PDB-2o57: Crystal Structure of a putative sarcosine dimethylglycine methylt...

ID or keywords:

Entry

Database: PDB / ID: 2o57

Title

Crystal Structure of a putative sarcosine dimethylglycine methyltransferase from Galdieria sulphuraria

Components

putative sarcosine dimethylglycine methyltransferase

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Protein Structure Initiative / PSI-2 / Center for Eukaryotic Structural Genomics / CESG

Function / homology

Mycolic acid cyclopropane synthase domain like / Vaccinia Virus protein VP39 / Helix Hairpins / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta

Function and homology information

Biological species

Galdieria sulphuraria (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.946 Å

Authors

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

Citation

Journal: To be Published
Title: Crystal Structure of a putative sarcosine dimethylglycine methyltransferase from Galdieria sulphuraria
Authors: Mccoy, J.G. / Wesenberg, G.E. / Phillips Jr., G.N. / Bitto, E. / Bingman, C.A.

History

Deposition	Dec 5, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 19, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4	Dec 27, 2023	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Remark 999

SEQUENCE The sequence of the protein is not available at the UNP database at the time of processing.

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2o57.cif.gz	250 KB	Display	PDBx/mmCIF format
PDB format	pdb2o57.ent.gz	200.5 KB	Display	PDB format
PDBx/mmJSON format	2o57.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2o57_validation.pdf.gz	455.8 KB	Display	wwPDB validaton report
Full document	2o57_full_validation.pdf.gz	468.4 KB	Display
Data in XML	2o57_validation.xml.gz	51 KB	Display
Data in CIF	2o57_validation.cif.gz	76.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o5/2o57 ftp://data.pdbj.org/pub/pdb/validation_reports/o5/2o57	HTTPS FTP

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Related structure data

Similar structure data	1zjp-2 2o1f-2 1wt2-2 1wt1-2 1zi5-2 1ziz-2 4fra-1 5tjl-2 1zj3-2 2a8u-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: GO.80048

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: putative sarcosine dimethylglycine methyltransferase

B: putative sarcosine dimethylglycine methyltransferase

C: putative sarcosine dimethylglycine methyltransferase

D: putative sarcosine dimethylglycine methyltransferase

135 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: putative sarcosine dimethylglycine methyltransferase

B: putative sarcosine dimethylglycine methyltransferase

defined by author&software
67.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: putative sarcosine dimethylglycine methyltransferase

D: putative sarcosine dimethylglycine methyltransferase

defined by author&software
67.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	97.541, 291.433, 86.340
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Details

The biological unit is a dimer. There are 2 biological units in the asymmetric unit (chains A & B and chains C & D).

#1: Protein	putative sarcosine dimethylglycine methyltransferase Mass: 33734.117 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Galdieria sulphuraria (eukaryote) / Gene: C1006_101305G20.T1 (MSU_GALDI) / Plasmid: PVP 16 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2)
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1042 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.3 Å³/Da / Density % sol: 46.2 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Protein Solution (10 MG/ML protein, 0.050 M sodium chloride, 0.0031 M sodium azide, 0.0003 M TCEP, 0.005 M Bis Tris pH 7.0) mixed in a 1:1 ratio with the Well Solution (23% MEPEG 5K, 0.03 M ...Details: Protein Solution (10 MG/ML protein, 0.050 M sodium chloride, 0.0031 M sodium azide, 0.0003 M TCEP, 0.005 M Bis Tris pH 7.0) mixed in a 1:1 ratio with the Well Solution (23% MEPEG 5K, 0.03 M sarcosine, 0.1 M MOPS pH 7.0), Cryoprotected with: well solution supplemented with up to 15% glycerol, vapor diffusion, hanging drop, temperature 293K

Crystal

Density Matthews: 2.3 Å³/Da / Density % sol: 46.2 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, hanging drop
Details: Protein Solution (10 MG/ML protein, 0.050 M sodium chloride, 0.0031 M sodium azide, 0.0003 M TCEP, 0.005 M Bis Tris pH 7.0) mixed in a 1:1 ratio with the Well Solution (23% MEPEG 5K, 0.03 M ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-D / Wavelength: 0.97923, 0.96400

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 8, 2006 / Details: Adjustable focusing mirrors in K-B geometry

Radiation

Monochromator: Si(111) Double Crystal Monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97923	1
2	0.964	1

Reflection

Resolution: 1.95→50 Å / Num. obs: 89709 / % possible obs: 99.4 % / Redundancy: 7.2 % / R_merge(I) obs: 0.11 / Χ²: 1.001 / Net I/σ(I): 7.618

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	Χ²	% possible all
1.95-2.02	5.1	0.597	1.775	8471	0.846	95
2.02-2.1	6.8	0.476		8901	0.9	99.7
2.1-2.2	7.5	0.372		8916	0.92	100
2.2-2.31	7.6	0.274		8956	0.989	100
2.31-2.46	7.6	0.219		8981	1.071	100
2.46-2.65	7.6	0.178		8972	1.081	100
2.65-2.91	7.6	0.136		8993	1.073	100
2.91-3.33	7.6	0.093		9057	1.024	100
3.33-4.2	7.5	0.079		9106	1.021	100
4.2-48.771	7.3	0.066		9356	1.006	99.6

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Phasing

Phasing

Method:

MAD

Phasing MAD set

Highest resolution: 1.95 Å / Lowest resolution: 46.25 Å

ID	R cullis acentric	R cullis centric	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	0	0	0	0	83129	6274
ISO_2	0.64	0.625	1.264	1.081	82443	6254
ANO_1	0.673	0	1.622	0	82310	0
ANO_2	0.784	0	1.177	0	82387	0

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	8.58-46.25	0	0	0	0	848	288
ISO_1	6.12-8.58	0	0	0	0	1630	317
ISO_1	5.01-6.12	0	0	0	0	2155	318
ISO_1	4.34-5.01	0	0	0	0	2560	319
ISO_1	3.89-4.34	0	0	0	0	2932	322
ISO_1	3.55-3.89	0	0	0	0	3252	317
ISO_1	3.29-3.55	0	0	0	0	3544	318
ISO_1	3.08-3.29	0	0	0	0	3810	318
ISO_1	2.9-3.08	0	0	0	0	4082	318
ISO_1	2.76-2.9	0	0	0	0	4323	320
ISO_1	2.63-2.76	0	0	0	0	4547	323
ISO_1	2.52-2.63	0	0	0	0	4735	313
ISO_1	2.42-2.52	0	0	0	0	5000	325
ISO_1	2.33-2.42	0	0	0	0	5155	305
ISO_1	2.25-2.33	0	0	0	0	5388	333
ISO_1	2.18-2.25	0	0	0	0	5543	313
ISO_1	2.11-2.18	0	0	0	0	5760	319
ISO_1	2.06-2.11	0	0	0	0	5895	320
ISO_1	2-2.06	0	0	0	0	6037	301
ISO_1	1.95-2	0	0	0	0	5933	267
ANO_1	8.58-46.25	0.387	0	3.651	0	846	0
ANO_1	6.12-8.58	0.321	0	4.164	0	1630	0
ANO_1	5.01-6.12	0.337	0	3.936	0	2155	0
ANO_1	4.34-5.01	0.475	0	2.784	0	2560	0
ANO_1	3.89-4.34	0.458	0	2.871	0	2932	0
ANO_1	3.55-3.89	0.495	0	2.609	0	3252	0
ANO_1	3.29-3.55	0.521	0	2.348	0	3544	0
ANO_1	3.08-3.29	0.505	0	2.428	0	3810	0
ANO_1	2.9-3.08	0.554	0	2.164	0	4082	0
ANO_1	2.76-2.9	0.592	0	1.899	0	4323	0
ANO_1	2.63-2.76	0.661	0	1.626	0	4547	0
ANO_1	2.52-2.63	0.693	0	1.485	0	4735	0
ANO_1	2.42-2.52	0.752	0	1.294	0	5000	0
ANO_1	2.33-2.42	0.795	0	1.138	0	5155	0
ANO_1	2.25-2.33	0.838	0	0.966	0	5388	0
ANO_1	2.18-2.25	0.892	0	0.853	0	5543	0
ANO_1	2.11-2.18	0.913	0	0.76	0	5760	0
ANO_1	2.06-2.11	0.933	0	0.67	0	5891	0
ANO_1	2-2.06	0.973	0	0.624	0	5906	0
ANO_1	1.95-2	0.988	0	0.591	0	5251	0
ISO_2	8.58-46.25	0.395	0.388	3.312	2.345	845	287
ISO_2	6.12-8.58	0.421	0.419	3.226	2.111	1630	317
ISO_2	5.01-6.12	0.466	0.459	2.818	2.286	2155	318
ISO_2	4.34-5.01	0.562	0.635	1.938	1.386	2560	319
ISO_2	3.89-4.34	0.604	0.62	1.829	1.158	2932	322
ISO_2	3.55-3.89	0.63	0.661	1.633	1.022	3252	317
ISO_2	3.29-3.55	0.659	0.638	1.581	1.052	3544	318
ISO_2	3.08-3.29	0.617	0.639	1.571	1.018	3810	318
ISO_2	2.9-3.08	0.624	0.622	1.535	0.971	4082	318
ISO_2	2.76-2.9	0.628	0.656	1.442	1.001	4323	320
ISO_2	2.63-2.76	0.642	0.636	1.355	0.864	4547	323
ISO_2	2.52-2.63	0.642	0.698	1.228	0.884	4735	313
ISO_2	2.42-2.52	0.659	0.687	1.093	0.762	4999	325
ISO_2	2.33-2.42	0.665	0.683	0.987	0.642	5155	305
ISO_2	2.25-2.33	0.663	0.684	0.842	0.592	5388	333
ISO_2	2.18-2.25	0.67	0.716	0.733	0.484	5542	313
ISO_2	2.11-2.18	0.671	0.724	0.654	0.432	5760	319
ISO_2	2.06-2.11	0.667	0.74	0.577	0.376	5895	319
ISO_2	2-2.06	0.688	0.745	0.501	0.326	6034	301
ISO_2	1.95-2	0.737	0.762	0.423	0.301	5255	249
ANO_2	8.58-46.25	0.376	0	3.447	0	844	0
ANO_2	6.12-8.58	0.324	0	3.925	0	1630	0
ANO_2	5.01-6.12	0.345	0	3.777	0	2155	0
ANO_2	4.34-5.01	0.47	0	2.822	0	2560	0
ANO_2	3.89-4.34	0.469	0	2.861	0	2932	0
ANO_2	3.55-3.89	0.526	0	2.519	0	3252	0
ANO_2	3.29-3.55	0.557	0	2.249	0	3544	0
ANO_2	3.08-3.29	0.565	0	2.115	0	3810	0
ANO_2	2.9-3.08	0.638	0	1.755	0	4082	0
ANO_2	2.76-2.9	0.685	0	1.549	0	4323	0
ANO_2	2.63-2.76	0.756	0	1.332	0	4547	0
ANO_2	2.52-2.63	0.792	0	1.121	0	4735	0
ANO_2	2.42-2.52	0.839	0	0.952	0	4999	0
ANO_2	2.33-2.42	0.876	0	0.831	0	5155	0
ANO_2	2.25-2.33	0.914	0	0.703	0	5388	0
ANO_2	2.18-2.25	0.941	0	0.599	0	5542	0
ANO_2	2.11-2.18	0.951	0	0.524	0	5760	0
ANO_2	2.06-2.11	0.965	0	0.451	0	5895	0
ANO_2	2-2.06	0.983	0	0.398	0	6031	0
ANO_2	1.95-2	0.991	0	0.357	0	5203	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	72.39	-45.268	7.596	SE	26.63	1.25
2	37.866	-48.759	1.017	SE	21.7	1.13
3	16.739	-23.303	5.971	SE	23.93	1.19
4	-12.973	-49.156	6.679	SE	25.71	1.19
5	14.343	-120.704	2.318	SE	25.51	1.16
6	28.248	-27.663	8.977	SE	26.34	1.17
7	23.541	-50.298	11.99	SE	26.73	1.12
8	28.066	-44.907	8.06	SE	28.67	1.15
9	75.354	-22.304	10.801	SE	32.28	1.15
10	14.397	-60.332	3.102	SE	24.83	1.06
11	71.889	-28.055	6.331	SE	31.58	1.24
12	14.452	-83.394	2.845	SE	26.32	1.1
13	67.645	-29.73	3.49	SE	30.1	1.07
14	-32.201	-108.501	7.66	SE	28.41	0.97
15	-8.719	-134.134	-0.213	SE	24.46	1.13
16	77.475	-43.788	8.081	SE	28.99	1.09
17	33.903	-22.619	11.826	SE	30.94	1.13
18	66.829	-50.603	9.579	SE	34.91	1.11
19	-14.807	-112.214	10.366	SE	24.63	0.89
20	23.179	-28.906	8.631	SE	29.42	1.08
21	21.289	-105.668	12.605	SE	31.96	0.87
22	32.844	-43.574	6.03	SE	30.1	1.07
23	37.631	-110.3	6.834	SE	31.71	0.78
24	85.982	-9.763	3.816	SE	49.39	0.9
25	-27.463	-40.183	-9.663	SE	60.73	0.5
26	-13.352	-35.287	-4.623	SE	43.74	0.42
27	-23.322	-19.992	-75.867	SE	35.8	0.11
28	-18.094	-37.799	-38.439	SE	33.69	0.15
29	-33.24	-33.328	-35.233	SE	39.46	0.34
30	-12.358	-51.992	-78.595	SE	19.78	0.07

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 89403

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
10.57-100	46.9	0.877	613
7.47-10.57	43	0.946	1100
6.1-7.47	42.2	0.929	1395
5.29-6.1	41.8	0.933	1646
4.73-5.29	41.4	0.948	1838
4.32-4.73	42.9	0.947	2009
4-4.32	42.1	0.947	2199
3.74-4	43.2	0.94	2328
3.52-3.74	45.6	0.935	2511
3.34-3.52	47.4	0.93	2598
3.19-3.34	47.9	0.922	2779
3.05-3.19	49.1	0.917	2872
2.93-3.05	48.5	0.91	3000
2.82-2.93	51	0.909	3116
2.73-2.82	50.6	0.906	3220
2.64-2.73	54.6	0.902	3302
2.56-2.64	54.5	0.904	3419
2.49-2.56	54.7	0.901	3523
2.42-2.49	57.1	0.898	3631
2.36-2.42	58.2	0.897	3704
2.31-2.36	60.9	0.905	3829
2.25-2.31	61.3	0.9	3883
2.2-2.25	64.9	0.903	3959
2.16-2.2	67.8	0.9	4077
2.11-2.16	69.1	0.892	4169
2.07-2.11	70.4	0.893	4188
2.03-2.07	72.6	0.878	4330
2-2.03	78.4	0.849	4335
1.95-2	80.1	0.798	5830

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
DM	5	phasing
REFMAC	5.2.0005	refinement
PDB_EXTRACT	2	data extraction
HKL-2000		data reduction

Refinement

Method to determine structure:

MAD / Resolution: 1.946→48.771 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.935 / WR_factor R_free: 0.225 / WR_factor R_work: 0.168 / SU B: 6.616 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.221	4502	5.02 %	RANDOM
R_work	0.166	-	-	-
obs	0.168	89679	99.242 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 21.559 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.295 Å²	0 Å²	0 Å²
2-	-	-0.701 Å²	0 Å²
3-	-	-	0.406 Å²

Refinement step

Cycle: LAST / Resolution: 1.946→48.771 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8744	0	0	1042	9786

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	8939
X-RAY DIFFRACTION	r_angle_refined_deg	1.452	1.958	12053
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.026	5	1106
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.257	23.759	439
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.913	15	1604
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.467	15	70
X-RAY DIFFRACTION	r_chiral_restr	0.105	0.2	1266
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	6842
X-RAY DIFFRACTION	r_nbd_refined	0.206	0.2	4484
X-RAY DIFFRACTION	r_nbtor_refined	0.302	0.2	6105
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.155	0.2	928
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.223	0.2	94
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.141	0.2	48
X-RAY DIFFRACTION	r_mcbond_it	0.848	1.5	5644
X-RAY DIFFRACTION	r_mcangle_it	1.352	2	8700
X-RAY DIFFRACTION	r_scbond_it	2.305	3	3831
X-RAY DIFFRACTION	r_scangle_it	3.445	4.5	3343

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	Num. reflection all	% reflection obs (%)
1.946-1.997	0.308	290	0.23	5730	6606	91.129
1.997-2.052	0.266	322	0.199	6080	6452	99.225
2.052-2.111	0.231	290	0.175	5998	6290	99.968
2.111-2.176	0.223	295	0.169	5795	6090	100
2.176-2.247	0.233	306	0.165	5592	5899	99.983
2.247-2.326	0.209	321	0.164	5426	5747	100
2.326-2.414	0.214	285	0.164	5220	5505	100
2.414-2.513	0.227	295	0.168	5057	5352	100
2.513-2.624	0.241	214	0.173	4874	5089	99.98
2.624-2.752	0.228	254	0.172	4652	4906	100
2.752-2.901	0.225	220	0.169	4440	4660	100
2.901-3.077	0.239	232	0.17	4201	4433	100
3.077-3.289	0.237	206	0.166	3940	4146	100
3.289-3.553	0.225	202	0.153	3683	3885	100
3.553-3.892	0.191	183	0.144	3410	3593	100
3.892-4.351	0.198	169	0.141	3093	3262	100
4.351-5.023	0.178	138	0.147	2762	2900	100
5.023-6.15	0.247	127	0.192	2338	2465	100
6.15-8.69	0.213	97	0.185	1848	1948	99.846
8.69-48.771	0.21	56	0.177	1038	1136	96.303

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