PDB-4hg2: The Structure of a Putative Type II Methyltransferase from Anaero...

ID or keywords:

Entry

Database: PDB / ID: 4hg2

Title

The Structure of a Putative Type II Methyltransferase from Anaeromyxobacter dehalogenans.

Components

Methyltransferase type 11

Keywords

TRANSFERASE /

Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Program for the Characterization of Secreted Effector Proteins / PCSEP /

S-adenosylmethionine / AdoMet_MTases

Function / homology

Function and homology information

methyltransferase activity /

Biological species

Anaeromyxobacter dehalogenans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.6 Å

Authors

Cuff, M.E. / Chhor, G. / Clancy, S. / Brown, R.N. / Cort, J.R. / Heffron, F. / Nakayasu, E.S. / Adkins, J.N. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Program for the Characterization of Secreted Effector Proteins (PCSEP)

Citation

Journal: TO BE PUBLISHED
Title: The Structure of a Putative Type II Methyltransferase from Anaeromyxobacter dehalogenans.
Authors: Cuff, M.E. / Chhor, G. / Clancy, S. / Brown, R.N. / Cort, J.R. / Heffron, F. / Nakayasu, E.S. / Adkins, J.N. / Joachimiak, A.

History

Deposition	Oct 5, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 17, 2012	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2017	Group: Data collection / Refinement description / Category: diffrn_radiation / software / Item: _diffrn_radiation.pdbx_diffrn_protocol

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4hg2.cif.gz	214.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4hg2.ent.gz	179.6 KB	Display	PDB format
PDBx/mmJSON format	4hg2.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/hg/4hg2 ftp://data.pdbj.org/pub/pdb/validation_reports/hg/4hg2	HTTPS FTP

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Related structure data

Similar structure data	2x81-d 4my6-d 2i1a-1 2o1m-2 6p5h-d 5x0f-d 5knj-1 1j6r-1 5id8-3 3h9f-d 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 - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: MCSG-apc102431

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Methyltransferase type 11

B: Methyltransferase type 11

hetero molecules

57.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Methyltransferase type 11

hetero molecules

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

2

B: Methyltransferase type 11

hetero molecules

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

Unit cell

Length a, b, c (Å)	48.067, 88.447, 64.664
Angle α, β, γ (deg.)	90.000, 91.990, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Details

THE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

#1: Protein	Methyltransferase type 11 Mass: 28578.996 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anaeromyxobacter dehalogenans (bacteria) Strain: 2CP-C / Gene: Adeh_3042 / Plasmid: pMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q2IE03
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer) Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 722 / 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: 2.4 Å³/Da / Density % sol: 48.82 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M MES pH 6.5, 12% PEG 20K, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97915 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 9, 2012

Radiation

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

Radiation wavelength

Wavelength: 0.97915 Å / Relative weight: 1

Reflection

Redundancy: 4.1 % / Av σ(I) over netI: 18.91 / Number: 294290 / R_merge(I) obs: 0.086 / Χ²: 1.13 / D res high: 1.6 Å / D res low: 50 Å / Num. obs: 71301 / % possible obs: 99.9

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
4.34	50	97.7	1	0.055	2.435	4
3.45	4.34	99.8	1	0.051	2.085	4
3.01	3.45	99.9	1	0.064	2.147	4
2.74	3.01	99.9	1	0.075	1.949	4.1
2.54	2.74	100	1	0.083	1.679	4.1
2.39	2.54	100	1	0.085	1.388	4.2
2.27	2.39	100	1	0.092	1.254	4.2
2.17	2.27	100	1	0.096	1.173	4.2
2.09	2.17	100	1	0.107	1.059	4.2
2.02	2.09	100	1	0.121	0.968	4.2
1.95	2.02	100	1	0.141	0.879	4.2
1.9	1.95	100	1	0.162	0.783	4.2
1.85	1.9	100	1	0.201	0.694	4.2
1.8	1.85	100	1	0.242	0.67	4.2
1.76	1.8	100	1	0.29	0.629	4.2
1.72	1.76	100	1	0.335	0.573	4.1
1.69	1.72	100	1	0.387	0.59	4.1
1.66	1.69	100	1	0.48	0.585	4.1
1.63	1.66	100	1	0.538	0.645	4.1
1.6	1.63	100	1	0.635	0.508	4.1

Reflection

Resolution: 1.6→50 Å / Num. all: 71301 / Num. obs: 71301 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / B_iso Wilson estimate: 17 Å² / R_merge(I) obs: 0.086 / Χ²: 1.127 / Net I/σ(I): 7.6

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.6-1.63	4.1	0.635	3554	0.508	1	100
1.63-1.66	4.1	0.538	3589	0.645	1	100
1.66-1.69	4.1	0.48	3494	0.585	1	100
1.69-1.72	4.1	0.387	3608	0.59	1	100
1.72-1.76	4.1	0.335	3537	0.573	1	100
1.76-1.8	4.2	0.29	3584	0.629	1	100
1.8-1.85	4.2	0.242	3557	0.67	1	100
1.85-1.9	4.2	0.201	3525	0.694	1	100
1.9-1.95	4.2	0.162	3564	0.783	1	100
1.95-2.02	4.2	0.141	3591	0.879	1	100
2.02-2.09	4.2	0.121	3550	0.968	1	100
2.09-2.17	4.2	0.107	3544	1.059	1	100
2.17-2.27	4.2	0.096	3573	1.173	1	100
2.27-2.39	4.2	0.092	3579	1.254	1	100
2.39-2.54	4.2	0.085	3567	1.388	1	100
2.54-2.74	4.1	0.083	3558	1.679	1	100
2.74-3.01	4.1	0.075	3588	1.949	1	99.9
3.01-3.45	4	0.064	3591	2.147	1	99.9
3.45-4.34	4	0.051	3581	2.085	1	99.8
4.34-50	4	0.055	3567	2.435	1	97.7

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC		refinement
PDB_EXTRACT	3.11	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
SHELXD		phasing
SHELXE		model building
MLPHARE		phasing
DM		phasing
SOLVE		phasing
RESOLVE		phasing
ARP/wARP		model building
CCP4		phasing
O		model building
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 1.6→30.35 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.96 / WR_factor R_free: 0.18 / WR_factor R_work: 0.1549 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9066 / SU B: 2.847 / SU ML: 0.051 / SU R Cruickshank DPI: 0.0765 / SU R_free: 0.0764 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.076
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1786	3594	5.1 %	RANDOM
R_work	0.1521	-	-	-
all	0.1535	71051	-	-
obs	0.1535	71051	99.76 %	-

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: 62.46 Å² / B_iso mean: 20.3055 Å² / B_iso min: 8.22 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.09 Å²	0 Å²	-0.04 Å²
2-	-	0.77 Å²	0 Å²
3-	-	-	-0.68 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→30.35 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3690	0	44	722	4456

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.019	4067
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	3828
X-RAY DIFFRACTION	r_angle_refined_deg	1.791	1.964	5580
X-RAY DIFFRACTION	r_angle_other_deg	1.058	3.005	8756
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.349	5	508
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.645	20.408	196
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.29	15	559
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.128	15	64
X-RAY DIFFRACTION	r_chiral_restr	0.109	0.2	574
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.021	4697
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1023

LS refinement shell

Resolution: 1.6→1.641 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.278	259	-
R_work	0.223	4966	-
all	-	5225	-
obs	-	-	99.9 %

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	0.4187	-0.0672	0.0141	0.4889	-0.0281	0.9205	-0.0102	0.0025	-0.025	0.0153	0.0309	0.022	0.1077	-0.0349	-0.0207	0.06	-0.0048	-0.0003	0.0128	-0.0006	0.0748	31.8164	26.4213	10.352
2	1.271	0.1218	-0.0465	0.8928	-0.6949	2.5477	0.0104	-0.0819	0.0923	-0.0065	-0.077	0.0283	-0.0563	-0.1108	0.0666	0.0887	0.002	-0.0025	0.025	-0.0182	0.1208	12.0871	46.5377	4.6144
3	0.6634	-0.0234	0.831	0.4625	0.0958	1.868	-0.0043	0.0087	-0.0046	0.0208	-0.0037	0.0114	-0.0389	0.0167	0.008	0.0545	0.0013	0.003	0.0005	0.004	0.0804	30.314	40.2609	10.4358
4	2.1913	0.3911	-1.9039	0.4255	-0.1288	1.8087	-0.0312	0.0814	0.039	-0.0133	-0.0093	0.1159	0.0713	-0.113	0.0405	0.099	-0.0127	-0.0109	0.0784	-0.0103	0.143	7.6646	38.4381	0.9883
5	4.3121	-3.4032	-0.8616	3.562	2.4801	4.984	0.0437	0.1381	0.1236	-0.1098	-0.0632	-0.0011	0.0243	-0.2821	0.0195	0.1321	-0.0252	-0.0492	0.1284	0.0437	0.1245	10.4133	44.9797	-11.3179
6	1.0495	-0.1872	1.1067	0.3641	0.0495	1.3701	-0.0155	0.1054	0.0569	-0.0267	-0.0157	-0.0224	-0.0656	0.1227	0.0312	0.066	-0.0101	0.0008	0.0225	0.0032	0.0866	32.3603	38.532	6.4464
7	0.7942	0.4207	-0.1476	0.3548	-0.2205	1.1732	0.0422	-0.0664	0.0198	0.042	-0.0379	-0.0077	-0.0607	0.0017	-0.0043	0.0822	0.003	0.0012	0.0233	-0.0042	0.0653	20.0838	65.7645	28.3716
8	2.0426	0.9837	0.6176	1.5247	0.0609	4.9992	-0.0295	-0.0274	0.1132	0.066	0.0522	0.1573	-0.4892	-0.3087	-0.0227	0.1309	0.0591	0.0192	0.0305	0.0043	0.0897	12.4127	76.3735	23.2752
9	0.1835	0.157	-0.0666	0.7391	-0.2703	0.9779	-0.0147	0.0503	0.0189	-0.0307	0.0103	0.0084	0.0055	-0.0229	0.0044	0.0688	0.0018	0.0014	0.0331	0.0047	0.0762	18.8841	65.0158	14.9098
10	1.697	-0.1601	1.2183	0.5579	-0.8462	3.1199	0.127	0.1161	-0.0813	0.0664	-0.0491	-0.006	0.1833	0.0376	-0.0779	0.1363	-0.0331	-0.0201	0.0346	-0.0133	0.109	-0.349	46.6869	26.6767
11	0.4719	-0.0132	-0.5979	0.8467	0.4929	1.152	-0.0006	0.0027	-0.0802	0.0112	-0.0969	-0.016	0.0391	-0.0493	0.0975	0.0734	-0.0011	-0.003	0.0225	-0.0096	0.0969	16.7526	53.3089	21.328
12	0.2017	0.1574	0.2528	0.5712	0.0568	0.3951	0.0849	-0.0795	-0.0133	0.0832	-0.0632	0.0638	0.0447	-0.1197	-0.0217	0.1321	-0.0122	-0.0082	0.0759	-0.0016	0.1106	2.7063	53.3767	30.6424

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	17 - 138
2	X-RAY DIFFRACTION	2	A	139 - 162
3	X-RAY DIFFRACTION	3	A	163 - 190
4	X-RAY DIFFRACTION	4	A	191 - 218
5	X-RAY DIFFRACTION	5	A	219 - 233
6	X-RAY DIFFRACTION	6	A	234 - 251
7	X-RAY DIFFRACTION	7	B	17 - 61
8	X-RAY DIFFRACTION	8	B	62 - 86
9	X-RAY DIFFRACTION	9	B	87 - 136
10	X-RAY DIFFRACTION	10	B	137 - 162
11	X-RAY DIFFRACTION	11	B	163 - 189
12	X-RAY DIFFRACTION	12	B	190 - 252

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