PDB-4yyc: Crystal structure of trimethylamine methyltransferase from Sinorh...

ID or keywords:

Entry

Database: PDB / ID: 4yyc

Title

Crystal structure of trimethylamine methyltransferase from Sinorhizobium meliloti in complex with unknown ligand

Components

Putative trimethylamine methyltransferase

Keywords

TRANSFERASE / New York Structural Genomics Research Consortium / NYSGRC / trimethylamine methyltransferase / unknown ligand / PSI-Biology

Function / homology

Function and homology information

methanogenesis / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation
Similarity search - Function

Biological species

Rhizobium meliloti (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.56 Å

Authors

Shabalin, I.G. / Porebski, P.J. / Gasiorowska, O.A. / Handing, K.B. / Niedzialkowska, E. / Cymborowski, M.T. / Cooper, D.R. / Stead, M. / Hammonds, J. / Ahmed, M. ...

Funding support

United States, 1items

Citation

Journal: Protein Sci. / Year: 2016
Title: Protein purification and crystallization artifacts: The tale usually not told.
Authors: Niedzialkowska, E. / Gasiorowska, O. / Handing, K.B. / Majorek, K.A. / Porebski, P.J. / Shabalin, I.G. / Zasadzinska, E. / Cymborowski, M. / Minor, W.

History

Deposition	Mar 23, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 8, 2015	Provider: repository / Type: Initial release
Revision 1.1	Mar 30, 2016	Group: Other
Revision 1.2	Jun 1, 2016	Group: Database references
Revision 1.3	Sep 27, 2017	Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4	Dec 4, 2019	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_special_symmetry / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Apr 13, 2022	Group: Database references / Structure summary / Category: audit_author / citation_author / database_2 Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4yyc.cif.gz	207 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4yyc_validation.pdf.gz	429.6 KB	Display	wwPDB validaton report
Full document	4yyc_full_validation.pdf.gz	432 KB	Display
Data in XML	4yyc_validation.xml.gz	23.7 KB	Display
Data in CIF	4yyc_validation.cif.gz	36.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yy/4yyc ftp://data.pdbj.org/pub/pdb/validation_reports/yy/4yyc	HTTPS FTP

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Related structure data

Related structure data	4tnnC 4znzC C: citing same article (ref.)
Similar structure data	2qne-d 5ij0-d 5iic-d 5syf-d 5ucy-d 4dgt-2 6pt9-d 5syc-d 6pt4-d 4k2b-d Search similar-shape structures by Omokage search (details) 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	TargetTrack: NYSGRC-022189

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#137 - May 2011 Cytochrome bc1 similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1)

Deposited unit

A: Putative trimethylamine methyltransferase

hetero molecules

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

1

A: Putative trimethylamine methyltransferase

hetero molecules

A: Putative trimethylamine methyltransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	89.162, 60.025, 88.345
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-479- ARG

#1: Protein	Putative trimethylamine methyltransferase Mass: 57871.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhizobium meliloti (bacteria) / Strain: 1021 / Gene: mttB, R01976, SMc04330 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q92P20
#2: Chemical	ChemComp-UNL / UNKNOWN LIGAND Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 525 / 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: 2.17 Å³/Da / Density % sol: 43.4 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 ul of 14 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG-I condition #33 (32%w/v PEG 4K, 0.1M Tris ...Details: 0.2 ul of 14 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG-I condition #33 (32%w/v PEG 4K, 0.1M Tris HCl, 0.8 M Lithium Chloride, pH=8.5) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was mixed with 1/15 v/v of 1 mg/ml TEV protease solution

Crystal

Density Matthews: 2.17 Å³/Da / Density % sol: 43.4 %

Crystal grow

Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 ul of 14 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG-I condition #33 (32%w/v PEG 4K, 0.1M Tris ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-D / Wavelength: 1.07808 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 6, 2014 / Details: Bimorph K-B pair

Radiation

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

Radiation wavelength

Wavelength: 1.07808 Å / Relative weight: 1

Reflection

Resolution: 1.56→50 Å / Num. obs: 67995 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / B_iso Wilson estimate: 19 Å² / R_merge(I) obs: 0.052 / R_pim(I) all: 0.027 / R_rim(I) all: 0.059 / R_sym value: 0.052 / Χ²: 1.109 / Net I/av σ(I): 28.051 / Net I/σ(I): 10.3 / Num. measured all: 315705

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.56-1.59	3.8	0.615	1.9	3289	0.806	0.344	0.71	0.784	97.4
1.59-1.62	4.6	0.583		3312	0.843	0.296	0.657	0.795	98.6
1.62-1.65	4.6	0.498		3335	0.893	0.254	0.561	0.83	99.1
1.65-1.68	4.6	0.419		3375	0.913	0.214	0.473	0.809	99.2
1.68-1.72	4.6	0.336		3368	0.946	0.171	0.379	0.819	99.1
1.72-1.76	4.6	0.292		3330	0.957	0.149	0.329	0.865	99.3
1.76-1.8	4.6	0.25		3373	0.958	0.128	0.282	0.885	99.5
1.8-1.85	4.7	0.208		3363	0.969	0.106	0.235	0.928	99.4
1.85-1.9	4.7	0.166		3362	0.982	0.085	0.188	0.941	99.4
1.9-1.97	4.7	0.14		3398	0.985	0.071	0.158	1.001	99.8
1.97-2.04	4.7	0.115		3382	0.99	0.059	0.129	1.079	99.8
2.04-2.12	4.7	0.093		3408	0.993	0.048	0.105	1.188	100
2.12-2.21	4.8	0.078		3414	0.995	0.039	0.087	1.209	100
2.21-2.33	4.8	0.064		3434	0.997	0.033	0.072	1.221	100
2.33-2.48	4.8	0.057		3405	0.997	0.029	0.064	1.285	100
2.48-2.67	4.8	0.053		3455	0.997	0.027	0.059	1.446	100
2.67-2.94	4.8	0.047		3435	0.997	0.024	0.053	1.67	100
2.94-3.36	4.8	0.035		3472	0.998	0.018	0.04	1.539	99.9
3.36-4.23	4.7	0.026		3503	0.999	0.013	0.029	1.363	99.5
4.23-50	4.5	0.025		3582	0.999	0.013	0.028	1.305	97.2

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Processing

Software

Name	Version	Classification
BLU-MAX		data collection
HKL-3000		data reduction
HKL-3000		phasing
HKL-3000		data scaling
SHELX		phasing
MLPHARE		phasing
REFMAC	5.8.0107	refinement
Coot		model building
PDB_EXTRACT	3.15	data extraction

Refinement

Method to determine structure:

SAD / Resolution: 1.56→50 Å / Cor.coef. F_o:F_c: 0.978 / Cor.coef. F_o:F_c free: 0.973 / WR_factor R_free: 0.1595 / WR_factor R_work: 0.1332 / FOM work R set: 0.8884 / SU B: 2.767 / SU ML: 0.048 / SU R Cruickshank DPI: 0.0665 / SU R_free: 0.0678 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1654	3363	5 %	RANDOM
R_work	0.1391	64442	-	-
obs	0.1403	64442	99.36 %	-

Solvent computation

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

Displacement parameters

B_iso max: 102.33 Å² / B_iso mean: 23.702 Å² / B_iso min: 11.29 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.22 Å²	0 Å²	-0 Å²
2-	-	1.01 Å²	0 Å²
3-	-	-	0.21 Å²

Refinement step

Cycle: final / Resolution: 1.56→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3651	0	8	530	4189
B_iso mean	-	-	25.45	35.72	-
Num. residues	-	-	-	-	479

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.019	3843
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	3637
X-RAY DIFFRACTION	r_angle_refined_deg	1.563	1.972	5231
X-RAY DIFFRACTION	r_angle_other_deg	0.96	3	8361
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.23	5	506
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.937	23.575	179
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.922	15	572
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.396	15	32
X-RAY DIFFRACTION	r_chiral_restr	0.097	0.2	572
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	4465
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	901
X-RAY DIFFRACTION	r_mcbond_it	0.625	1.077	1945
X-RAY DIFFRACTION	r_mcbond_other	0.623	1.075	1943
X-RAY DIFFRACTION	r_mcangle_it	1.036	1.61	2434

LS refinement shell

Resolution: 1.56→1.6 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.234	261	-
R_work	0.242	4621	-
all	-	4882	-
obs	-	-	97.8 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	1.1171	-0.1572	0.0839	0.7038	0.0287	0.6145	0.0283	-0.3136	-0.0134	0.0658	-0.0004	-0.0147	0.0108	0.063	-0.028	0.0793	-0.0285	0.0034	0.1875	0.0038	0.0304	21.9	0.4	35.101
2	0.7788	-0.0322	0.0828	0.2727	-0.1052	0.6582	0.0269	-0.0585	0.069	-0.0179	-0.0086	-0.0459	-0.0171	0.145	-0.0183	0.0569	-0.025	0.0114	0.1171	-0.0109	0.0494	26.413	6.055	20.474
3	8.8537	-1.0725	2.5468	0.1604	-0.1356	8.5712	0.2243	0.6039	-0.634	0.0262	-0.0937	0.0987	0.8401	0.2298	-0.1306	0.1919	0.0215	-0.0199	0.1139	-0.0395	0.1238	11.583	-11.489	19.026
4	0.7697	0.091	0.0152	0.1873	0.0024	0.2319	0.0317	-0.1103	0.1078	0.013	-0.0203	0.0127	-0.0545	0.0078	-0.0114	0.0798	-0.0115	0.0042	0.093	-0.0144	0.0521	3.951	5.974	23.224
5	66.2534	13.8945	37.893	6.75	-0.8826	42.0448	-1.3913	1.7957	2.8592	0.5983	0.2107	0.8006	-2.8728	1.5334	1.1806	0.7117	-0.201	0.0361	0.3843	0.0226	0.4662	-16.474	24.648	23.537
6	3.2872	0.7396	0.8081	0.3128	0.1501	0.6101	-0.0265	0.0912	0.2502	-0.0592	-0.0152	0.0094	-0.1155	0.0711	0.0417	0.0991	-0.0131	0.0133	0.0683	0.0383	0.0836	13.356	15.746	7.212

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	35 - 136
2	X-RAY DIFFRACTION	2	A	137 - 315
3	X-RAY DIFFRACTION	3	A	316 - 335
4	X-RAY DIFFRACTION	4	A	336 - 444
5	X-RAY DIFFRACTION	5	A	445 - 451
6	X-RAY DIFFRACTION	6	A	459 - 521

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